Bouboulina was born in a prison in Constantinople; she originated from the local native Arvanite population of the island of Hydra. She was the daughter of Stavrianos Pinotsis, a captain from Hydra island, and his wife Skevo. The Ottomans had imprisoned Pinotsis for his part in the failed Orlof Revolution of 1769–1770 against the Ottoman rule. During one of her mother's visits, she was born. Her father died soon afterward and the mother and child returned to Hydra. They moved to the island of Spetses four years later when her mother married Dimitrios Lazarou-Orlof. Bouboulina had eight half-siblings.