Seven Historical Mysteries Science Still Can't Fully Explain

Modern science has revolutionized how we investigate the past: researchers now extract DNA from ancient bones, use lidar and other remote-sensing tools to reveal buried settlements beneath dense canopy, and scan sealed artifacts noninvasively. Yet even with these advances, some well-documented historical puzzles resist definitive answers. Natural forces, human activity and gaps in the written record often erase the direct evidence needed to reach certainty.

Tunguska Airburst (1908)

On June 30, 1908, a massive explosion occurred over a remote area of Siberia near the Tunguska River, flattening an estimated 80 million trees across roughly 2,000 square kilometers. The blast produced seismic waves recorded across Eurasia and atmospheric disturbances observed as far away as Western Europe, but no undisputed impact crater or large meteorite fragments have been found.

The leading explanation is an atmospheric airburst from a stony asteroid or comet fragment. Computer models and field investigations largely support that scenario, but uncertainties remain about the object's size, composition and exact trajectory. Because physical evidence is limited, alternative hypotheses—such as a volatile-rich cometary fragment—still attract discussion among researchers.

Missing Tombs of Cleopatra VII and Alexander the Great

Despite extensive archaeological work around Alexandria, the burial sites of Cleopatra VII and Alexander the Great remain unconfirmed. Ancient writers claimed Cleopatra was interred with Mark Antony in a royal tomb near Alexandria, and Alexander’s body was said to have been brought to Egypt after his death in 323 BCE and publicly displayed in Alexandria.

Centuries of earthquakes, subsidence, coastal change, urban development and looting have radically altered the ancient city and shoreline. Excavations at candidate sites such as Taposiris Magna have produced intriguing traces but no definitive proof, leaving open the possibility that these tombs have been destroyed, deeply buried, or misidentified.

The Lost Roanoke Colony (Late 16th Century)

England’s Roanoke Colony, established in 1587 on what is now Roanoke Island, vanished sometime before Governor John White’s return from England in 1590. The settlement was abandoned without signs of a violent attack; the lone carved clue was the word "CROATOAN," apparently referring to a nearby island and its Indigenous inhabitants.

Archaeological work suggests the colonists may have dispersed, been absorbed into local communities, or migrated for resources after facing shortages, disease or tense relations. No single explanation fits all the evidence, and no confirmed remains of the settlers have been found, so Roanoke remains a striking example of early colonial fragility.

Vanished Complex Societies: Amazonia and the Indus Valley

For decades scholars assumed the Amazon could not host large, complex societies, but recent lidar surveys and excavations have revealed networks of roads, plazas, fortifications and managed landscapes hidden beneath the canopy—evidence that large populations once lived there. Why many of these societies declined or were transformed—whether from introduced disease after European contact, environmental pressures or social upheaval—remains debated.

The Indus Valley Civilization, one of the world’s earliest urban cultures, experienced a marked decline around 1900 BCE when many major cities were systematically abandoned rather than destroyed. Geological evidence points to shifting river courses and prolonged drought as major stresses, but the undeciphered Indus script limits our understanding of how societies responded politically and socially.

The Nazca Lines (c. 500 BCE–500 CE)

The Nazca Lines of southern Peru are hundreds of enormous geoglyphs—animals, plants, geometric shapes and long straight lines—best seen from the air. They were created by clearing darker surface stones to expose lighter soil beneath, a method preserved by the dry climate.

Leading interpretations link the figures to ritual activity, water-related ceremonies, pilgrimage routes or astronomical alignments. No single theory explains the full variety of designs, and the absence of written Nazca records means their precise cultural purpose remains uncertain.

Roopkund Lake Skeletons (Indian Himalayas)

Near the glacial Roopkund Lake, researchers have uncovered skeletal remains of hundreds of people. Radiocarbon dating and genetic analysis show these individuals did not die in a single incident but represent multiple groups arriving at different times and from diverse regions, in some cases separated by nearly a millennium.

One cluster dates to around the ninth century CE and may have been killed in a sudden severe weather event; large hailstones are a plausible cause of the observed skull fractures. Later remains may be pilgrims or travelers who died under different circumstances. While modern techniques have clarified parts of the Roopkund story, questions remain about why people repeatedly traveled to this remote, high-altitude location.

The Antikythera Mechanism (c. 100 BCE)

Recovered from a Hellenistic-era shipwreck, the Antikythera Mechanism is the most complex mechanical device known from antiquity. Its interlocking bronze gears modeled lunar and planetary cycles and could predict eclipses with remarkable precision.

X-ray tomography and other imaging methods have revealed inscriptions and gear trains far more sophisticated than once imagined, and researchers have largely reconstructed its functions. Still, crucial questions remain: who designed it, whether similar devices were widespread, and why that level of mechanical knowledge seems to have largely disappeared from the historical record for centuries.

Despite substantial progress from modern science, these seven cases show that compelling evidence can still stop short of definitive answers. Continued fieldwork and new technologies may close some gaps, but some elements of the past may always remain partly veiled.