Marine turtles declined worldwide before the early 1900's due to heavy exploitation by humans. However, many populations have begun to recover since the 2000's. Maintaining genetic diversity as well as conservation efforts are important for population recovery and resilience. Here, we investigated the genetic diversity of 28 green turtles from five regions of the North Pacific (Ogasawara, Western Pacific Islands, Southeast Asia, Hawaii, and Eastern Pacific) using whole-genome resequencing data. Diversity varied among populations, with the northernmost Ogasawara population having the lowest diversity. However, few turtles had runs of homozygosity (ROH) longer than 2 Mbp, reflecting coalescence tens of generations back in time, corresponding to the period of intense exploitation in Ogasawara. The historical demography reconstructed by multiple sequentially Markovian coalescent (MSMC) suggested that the genetic diversity of the Ogasawara population was gradually lost due to isolation after divergence from the ancestral population about one million years ago. The present results were unexpectedly inconsistent with the population trend in the 1900s, which suggested a severe decline in the number of nesting females and hatchlings. Genetic diversity may have been preserved in juveniles foraging in areas remote from Ogasawara and not under hunting pressure, contributing to potential resilience.