Understanding the distribution range across the life history of endangered animals is crucial for effective conservation and management planning. However, endangered migratory green turtles with straight carapace lengths (SCLs) of <35 cm have been rarely observed in the northwestern Pacific. Information on wild green turtles with an SCL of <35 cm in this region is therefore scarce. Historically, four individuals with an SCL of <35 cm from the Japanese coasts and an oceanic area in Japan have been reported. From 2011 to 2013, we collected nine turtles with an SCL of <35 cm from Japanese coasts and coastal waters. We reviewed the existing literature and compiled records of newly collected individuals and their mitochondrial deoxyribonucleic acid haplotypes. The combined total of 13 turtles had SCLs ranging from 6.2 to 28.0 cm. Molecular analyses of nine newly collected turtles indicated that most individuals had hatched at green turtle nesting sites on the Ogasawara Islands and islands in the Ryukyu Archipelago. These results suggest that early juvenile green turtles inhabit Japanese waters, and some turtles with an SCL of <35 cm appear to have remained in Japanese waters after leaving their natal beaches in Japan without drifting with the prevailing oceanic currents to central north or eastern Pacific regions. Although the sample size in the present study was small, this is a first step in constructing comprehensive conservation and management plans for green turtles in the northwestern Pacific.