Cyprus is an island steeped in history, a crossroads of civilizations where empires have risen and fallen, leaving behind a legacy of grandeur, conflict, and mystery. While much of its past has been carefully documented, there are chapters in its history that remain frustratingly incomplete—stories that refuse to be neatly filed into the annals of recorded time. From ancient cities with no known origins to shipwrecks whose final journeys remain a mystery, Cyprus is home to a wealth of historical puzzles that continue to baffle researchers.

Some mysteries are buried in the sands of time, while others are far more recent, yet equally confounding, still raising questions decades later. These stories share one thing in common: they have left behind more questions than answers.

Amathus, one of the most enigmatic ancient cities of Cyprus, stood apart from other city-kingdoms due to its uncertain origins. Unlike most settlements on the island, there is no evidence of a Bronze Age predecessor, and its foundation lacks a clear historical record. Despite this, the city flourished from the 11th century BC, maintaining a distinct cultural identity, including the use of the Eteocypriot language—an undeciphered script believed to predate Greek influence. Its rich copper deposits, fertile land, and strategic coastal location made it a key trading hub, with connections to both the Aegean and the Levant.

Adding to its mystery, Amathus was home to one of Cyprus’s most significant sanctuaries of Aphrodite, second only to Paphos. Excavations by the French School of Athens and the Department of Antiquities have revealed extensive cemeteries, defensive walls, and evidence of early funerary cult practices. However, many aspects of its foundation and development remain unresolved, making it one of Cyprus’s most perplexing archaeological sites.

Discovered in 2007 off the southern coast of Cyprus near the village of Mazotos, the Mazotos Shipwreck is a significant archaeological find dating back to the late Classical period, around the 4th century BC. The merchant vessel rests at a depth of approximately 45 meters and is notable for its well-preserved cargo of over 500 amphorae, predominantly from the island of Chios, indicating the transportation of Chian wine—a prized commodity in antiquity.

Ongoing excavations led by the Maritime Archaeological Research Laboratory (MARELab) of the University of Cyprus have provided valuable insights into ancient Mediterranean trade routes and shipbuilding techniques. In the 2018 excavation season, archaeologists uncovered 70 additional amphorae and parts of the ship's wooden hull, revealing construction methods that combined Greek and Phoenician techniques.

However, the cause of its sinking is still unknown, with theories ranging from storms and navigational errors to piracy, though no definitive evidence supports any single explanation. While its cargo of Chian amphorae suggests an origin from Chios, its final destination and complete trade route remain unclear. Was Cyprus its primary stop, or was it en route elsewhere in the Mediterranean? Additionally, the site has not been fully excavated, leaving open the possibility of uncovering artifacts—such as tools, navigational instruments, or personal items—that could shed more light on its voyage and crew.

Following the fall of Acre in 1291, the Knights Templar established a significant presence on the island of Cyprus, which had become the new base for Crusader operations. The island's strategic location made it a vital stronghold for the Templars after their loss of territories in the Holy Land.​

In 1307, under orders from Pope Clement V, the Templars across Europe were arrested and charged with heresy, blasphemy, and other serious accusations. In Cyprus, the Templars faced similar trials. The proceedings on the island were notably less severe compared to those in France, primarily due to the absence of torture and the relatively sympathetic local authorities. Many Templars in Cyprus confessed under duress, but these confessions were later retracted. The trials concluded without definitive evidence of wrongdoing, leading to the acquittal of many members. ​

Despite the lack of concrete evidence, the Papal bull Vox in excelso issued in 1312 officially dissolved the Knights Templar. Their properties and assets in Cyprus were transferred to the Knights Hospitaller, another military order. The dissolution marked the end of the Templars' influence on the island, but the fairness and legitimacy of the trials in Cyprus, as elsewhere, remain subjects of historical debate.

The Martyrs of Kantara remain a historical mystery due to the limited records surrounding their persecution and execution in 1231. These thirteen Orthodox monks, who resisted adopting the Catholic practice of using unleavened bread in the Eucharist, were arrested under orders from Pope Gregory IX and imprisoned for three years. While accounts confirm that one monk died in captivity and the remaining twelve were burned alive in Nicosia, the exact details of their trial, imprisonment conditions, and whether political motivations played a role remain unclear.

Adding to the mystery, most of what is known comes from the "Narratio of the Thirteen Martyrs," a text written decades later, raising questions about historical accuracy and possible embellishment. The broader struggle between Orthodox and Catholic factions in Lusignan-ruled Cyprus complicates the narrative, leaving scholars to debate whether their execution was purely religious persecution or part of a wider power struggle. Their martyrdom is commemorated in the Orthodox Church, but many aspects of their fate remain unresolved.

The discovery of a 9,000-year-old circular building in the Troodos Mountains has puzzled archaeologists, as its purpose remains unknown. Measuring 10 meters in diameter, the structure challenges previous assumptions about Cyprus’s early inhabitants, particularly in the mountainous hinterland, which was not believed to have complex settlements during this period. Unlike other Neolithic sites on the island, this building does not fit neatly into existing archaeological patterns, raising questions about its function—was it a communal gathering space, a ritual site, or something entirely different? Its unique characteristics and connection to the so-called "pig-farming phase" (ca. 6400-5600 B.C.) deepen the mystery, making it one of Cyprus’s most intriguing prehistoric enigmas. 

The assassination of Youssef Sebai in Nicosia, Cyprus, remains one of the island’s most politically charged mysteries. Sebai, a prominent Egyptian journalist, novelist, and close confidant of Egyptian President Anwar Sadat, was shot dead on February 18, 1978, at the Hilton Hotel during a pro-Palestinian conference. His murder triggered an international crisis when the assassins hijacked a plane and took hostages, leading to a failed Egyptian military intervention at Larnaca Airport that resulted in heavy casualties. 

While two men, allegedly linked to Palestinian extremist factions, were arrested and sentenced to life in Cyprus, their exact affiliations and motives remain uncertain. Theories suggest the murder was a direct response to Sadat’s peace overtures toward Israel, branding Sebai a "traitor" to the Palestinian cause. However, conflicting reports indicate possible involvement from intelligence agencies or other Middle Eastern political forces. The Cypriot government's refusal to extradite the killers further deepened suspicions, leaving key questions unanswered. Who truly orchestrated the assassination? Was it solely an extremist act, or part of a larger geopolitical scheme? Decades later, the case still holds unresolved elements, making it one of Cyprus’s enduring political mysteries.

In 1929, the village of Agia Eirini in Cyprus became the site of a remarkable archaeological discovery: over 2,000 terracotta figures arranged in semicircles around a central altar. These figures, dating from approximately 650 to 500 B.C., depict warriors, priests, chariots, and animals, offering a unique glimpse into ancient Cypriot religious practices.

The purpose and exact significance of this terracotta assembly remain subjects of scholarly debate. Some researchers suggest the figures were votive offerings in a fertility cult, while others propose they represent a warrior deity or communal ancestor worship. The precise rituals conducted at this sanctuary and the reasons for the site's eventual abandonment continue to intrigue archaeologists, making the terracotta army of Agia Eirini one of Cyprus's enduring archaeological mysteries.

Despite decades of research and excavation, many of Cyprus’ mysteries remain unresolved. Whether they stem from lost civilizations, unexplained rituals, or political intrigue, each of these puzzles adds another layer to the island’s rich and complex history. Some may never be fully explained, while others may one day reveal their secrets through new discoveries and advancements in technology. Until then, they continue to captivate scholars and history enthusiasts alike, ensuring that Cyprus remains a land of intrigue, where the past is never quite finished telling its story.