High altitude upland rice (Oryza sativa L.) production systems are expected to benefit from climate change induced increase in temperatures. The potential yield of rice genotypes is governed by the thermal environment experienced during crop development phases when yield components are determined. Thus, knowledge on genotypic variability in phenotypic responses to variable temperature is required for assessing the adaptability of rice production to changing climate. Although, several crop models are available for this task, genotypic thermal constants used to simulate crop phenology vary strongly among the models and are under debate. Therefore, we conducted field trials with ten contrasting upland rice (O. sativa L.) genotypes on three locations along an altitudinal gradient with five monthly staggered sowing dates for two years in Madagascar with the aim to study phenological responses at different temperature regimes. We found that, crop duration is equally influenced by genotype selection, sowing date and year in the high altitude. In contrast, in mid altitudes genotype has no effect on crop duration. At low altitudes crop duration is more affected by sowing date. Grain yield is strongly affected by low temperatures at high altitudes and severly influenced by frequent tropical cyclones at low altitudes. In high altitude, genotype explained 68% of variation in spikelet sterility, whereas in mid and low altitudes environment explained more than 70% of the variation. The phenological responses determining crop duration and yield, the basic genotypic thermal constants, and the analyses of genotypic thermal responses with regard to spikelet sterility reported here, provide valuable information for the improvement of rice phenological models urgently needed to develop new genotypes and better adapted cropping calendars.