Marine turtles are endangered megafauna that face both natural disturbances and anthropogenic threats. The islands of Wan-an and Lanyu support two important green turtle nesting populations in Taiwan and are separated by 250 km. Nesting activity was first documented on Wan-an Island in 1992, with 8 nesting females being documented. A further 11 nesting females were first documented on Lanyu Island in 1997. However, by 2015, the Wan-an Island population declined to only 2 nesting females, whereas the Lanyu Island population showed peaks in abundance (up to 24 nesters) every 3-5 years with no long-term decline. Additionally, the recruitment of new nesters to the Wan-an Island population decreased to 15%, whereas recruitment into the Lanyu Island population remained high (66%). The decrease of the nesting population on Wan-an Island might be due to illegal poaching on the high seas along the migratory corridor of the turtles, whereas the stable nesting population on Lanyu Island showed no evidence of such a threat. The two nesting populations use different migratory corridors to their foraging grounds, resulting in different fates of development in population trend.