To improve the fruit and seed productivity in hermaphrodite ‘Sunrise Solo’ and female ‘Wonder Flare’, we investigated seasonal variations in the frequency of sexually altered abnormal misshapen flowers (carpelloid and pentandoria flowers) and female sterile flowers, fruit and seed yield, pollen germination ability, and the reproductive function of pistils under greenhouse cultivation conditions in Okinawa, Japan. In ‘Sunrise Solo’, the percentages of abnormal misshapen flowers were 42–66% from July to October (average temperature: 25.6–30.5°C), though they were below 10% from February to March (14.6–16.8°C) and December to January (16.9–18.1°C). The percentages of female sterile flowers were low (below 10%) from March to November (16.8–30.5°C), but high (13–37%) from December to February (14.6–18.1°C). Seed and fruit yield increased in May (24.6°C) and November (19.4°C), but decreased from January to March (14.6–18.1°C) and July to September (28.2–30.5°C). Pollen germination rates (52–87%) were high from April to June (22.2–27.2°C) and October to November (19.4–25.6°C) and pollen tube length was long (208–272 μm) during the same periods, while the rates were low (5–32%) and the tube length was short (63–134 μm) from January to March (14.6–18.1°C); moreover, no germinated pollen was found from July to September (28.2–30.5°C). These results of the seasonal fluctuation in pollen germination ability were supported by pollen germination tests performed in an incubation chamber, i.e., pollen germination rates were high (72–80%) between 20 and 25°C, but low (0–56%) below 15°C and above 30°C; however, the pistils of ‘Sunrise Solo’ and ‘Wonder Flare’ retained their reproductive function even during the period of low (16.7°C) and high (29.5–30.5°C) temperatures, i.e., fruit and seed yields were improved by pollination using pollen (germination rate: about 35%) collected from plants cultivated in an open field during the high temperature period or pollen preserved at sub-zero temperatures during the low and high temperature periods. These results indicate that fruit and seed production in papaya under low or high temperature conditions is unfavorable for pollen germination, but could be improved by artificial pollination with preserved pollen.