A rare congenital anomaly in the form of sagittal clefting of the fifth lumbar vertebra was observed in the skeleton of a young adult female excavated from the Greek colonial site of Apollonia Pontica (5th to 3rd centuries BC) on the Bulgarian Black Sea coast. No compensatory changes had occurred to the adjacent vertebrae, and no other skeletal anomalies or pathological conditions were observed in the skeleton. This anomaly, the first of its kind documented in ancient Greek remains, was likely asymptomatic and of no clinical significance.