Cassava (Manihot esculenta Crantz) production has been constrained by biotic and abiotic factors, which could be solved by conventional breeding. However, cassava hybridization is difficult because many genotypes do not flower or set seeds and yet cassava sexual reproduction is essential for breeding programs. Consequently, this study was undertaken to identify agro ecologies in Uganda that best promote cassava flowering and seed set in order to facilitate breeding. Field evaluation of eight genotypes in randomized complete block design with three replications at three agro-ecologies of Uganda for two cropping seasons was conducted. Weather data were monitored and cassava flowering/seed set-related traits were collected at one-month interval commencing from 1.5 Months after planting. Results indicated that varieties previously categorized as high flowering and seed set performed differently than those identified as poor flowering and seed set, although with varying genotypic differences in each environment. Genotypes mean performances, additive main effect and multiplicative interaction and genotype main effect and genotype by environment interaction bi-plots model’ results indicated Rwebitaba in Western savannah grassland agro-ecology and Namulonge-NaCRRI in Lake Victoria Crescent agro-ecology as the most favorable environments for the performance of all the evaluated traits, and season one as the most favorable season. However, the most stable environment for all the evaluated traits was Abi-ZARDI. Conclusively, the high proportion of variation which occurred between genotypes and environments was explained by the genotypic variances. Dry months had poorer cassava flower initiation and development than wet months of the cropping season. Therefore, Abi-ZARDI in North-western savannah grassland agro-ecology and season one could be recommended for the establishment and timing of cassava breeding nursery.