In 1868, when the Meiji government occupied Edo, he refused to deliver warships to the government, and escaped to Hakodate with the fleet. They hope to found a state reigned by Tokugawa family in Hokkaido, but the Meiji government refused their request. In 25 December, they declared foundation of the Republic of Hokkaido (Ezo Kyowakoku 蝦夷共和国), and elected Enomoto as resident.
The next year, the Meiji Governmental Army and Navy invaded Hokkaido and defeated the former Shogunate Army and Navy of the Republic. 18 May 1869 the Republic gave in, and Hokkaido accepted the Meiji Emperor's rule.
Enomoto was forgiven for the crime in 1872 and appointed as the government official of the Hokkaido agency. In 1874, he was promoted to Vice Admiral of the newly established Imperial Japanese Navy, and dispatched to Russia as Minister Plenipotentiary. He successively held the high position of government, until he died.