Heterotrigona itama is a stingless bee species from Meliponini tribe. The bee collects nectar, pollen and resin to produce honey, bee bread, and propolis. The bee is also known to visit and collect nectar from various types of flowers but there are limited studies on why this species of bee prefers to visit certain types of flowers. This study was conducted to identify the nectar concentration in selected flowers favoured by H. itama and the relationship between the bee and the morphology of the flowers. Nectar was obtained from different species of flowers and the concentrations were measured using a digital refractometer. The tube length of each flower species and the tongue length of the bees were also measured. The results revealed that flowers preferred by H. itama have high nectar concentrations. The tube lengths of the preferred flowers were between 2.0 and 4.0 mm, which is compatible with the tongue length of the bee. This study revealed that both nectar concentration and flower morphology are important factors for the bees in choosing their food sources. The results from this study will benefit the beekeepers in the identification of flowers that should be planted in their farms to improve stingless bee beekeeping activities. Understanding the relationship between the bees and their flower preferences could also help us to understand the importance of conserving both the bee colonies and the various species of flowering plants to ensure the sustainability of flora and fauna in the ecosystem.