Both ‘Atago’ and ‘Shinkou’ are late-season japanese pear (Pyrus pyrifolia Nakai) cultivars with russet-brown fruit, and the progenies of crosses made between ‘Nijisseiki’ and unknown cultivars, but they display different growth habit, fruit size, and fruit quality. To clarify the difference in fruit development between the two cultivars, the levels of endogenous gibberellins (GA1, GA3, and GA4) and abscisic acid (ABA) in fruit were identified and quantified by gas chromatography/mass spectrometry, and a histological study of fruit was carried out. The results showed that cell number rather than cell size of mesocarp is responsible for the difference in fruit size between the two cultivars. Furthermore, analysis of endogenous bioactive gibberellins revealed that ‘Atago’ fruit has much higher levels of GA1, GA3, and GA4 than ‘Shinkou’ fruit during fruit development, particularly during the early period of fruit growth. However, ‘Shinkou’ has a much higher ABA level than ‘Atago’ during the early period of fruit development. Abscisic acid concentration remained at an extremely low level after the first production peak after anthesis in ‘Atago’ compared with ‘Shinkou’.