The Yaeyama Islands provide habitat for juvenile green turtles originating from various rookeries in the western Pacific. The sea turtle fishery has been declining since 2004 due to the retirement of sea turtle fishermen in the region. We investigated the population ecology of green turtles based on capture-mark-recapture data from 1995 to 2016. The effect of the past sea turtle fishery on the green turtle population was analyzed by comparing the population structure, growth and mortality rates during 19952003, with those of the population in 2004-2016. Mean straight carapace lengths of green turtles in 1995-2003 were 51.5 cm (SD = 10.9, range 34.0-102.4, N = 838), annual growth rates were 2.7 cm year(-1) (SD = 1.31, range 0.09-5.32, N = 50), and mortality rates were 0.25 year(-1) (95% CI 0.20-0.30). In comparison, mean straight carapace length of green turtles in 2004-2016 was 55.5 cm (SD = 12.1, range 6.2-96.5, N = 595), growth rates were 2.24 cm year(-1) (SD = 0.78, range 0.79-4.17, N = 67) and mortality rates were 0.15 year(-1) (95% CI 0.11-0.19). Carapace size increased and annual growth and mortality rates decreased after 2004. The increase in the number of larger-sized green turtles and the decrease in mortality rates were likely effects of the decline in the sea turtle fishery.