The present study aimed at evaluating the genetic variability of different germplasms and comparative effectiveness of morphological descriptors, floral and reproductive biology of three CPTs of annatto viz.,Tamil Nadu (green fruited), Kerala (red fruited), Karnataka (dark red fruited) at department of Forest Biology and Tree improvement, Forest College and Research Institute, Mettupalayam during 2017-19. A record on sequence of flowering ascends along the latitudes. The sequence of flowering is top to bottom (basipetal) that is the development, maturation or opening from the apex towards the base in the sequence. It commenced from the southern side to the south eastern side. The colour of the flower is whitish pink in Tamil Nadu, moderate pink in Karnataka and dark pink in Kerala and this floral colour polymorphism suggests that pollinators (mainly bumble bees and ants) are the primary selective agents which influence flower colour. The stain I-KI showed 95 % pollen viability and it is found that the viability of the pollen grains decreased after four hours from pollen dehiscence and tricolporate pollen was observed in annatto. The observation on fruit set indicated that bixa plant can have both self- and cross-pollination. Fruit maturity takes place 80 – 95 days counting from the day of pollination to fruit dehiscence. The shape of the fruit resembles rounded oblong pyriform. Maximum seed production was recorded in the red fruited (collected from Karnataka) (113.12 g) plant followed by the dark red fruited plant (Kerala) and the green fruited variant (TN).