The nesting habits, morphological and genetic structures of stingless bees were assessed using the traditional taxonomic characters and BLAST analysis results in 18 populations of Tetragonula in the Philippines. Different structures, shapes, and colors of stingless bee entrances were recorded. Dendrogram was drawn using the measurement derived from the morphometric characters. The majority of the species build their nest in tree cavities, cemented walls, and rocks with circular-shaped entrances. Irregularity in shapes of colonies from Ogbong (Catanduanes), Calapan (Oriental, Mindoro), Alabat, and Perez (Quezon) was observed. Most colony entrances are hard and dark in color, facing east with three to 15 guard bees. Light-colored entrances were observed in colonies from Cacilles (Hernani, Samar) and Pangi (Gasan, Marinduque). Nesting habits of stingless bee species were not species-specific. The only amplicon from 16S rRNA gene reproducible in 12 colonies was analyzed. No hits found in sampled specimen from Panim-an, Caramoan, Camarines Sur, and Oriental, Mindoro (Calapan and Naujan), but, samples from Tagbilaran, Bohol, and Tagum, Davao was confirmed. In Luzon, the identified species of stingless bees were Tetragonula iridipennis found in Alabat and Perez (Quezon), Gasan (Marinduque), Garchitorena (Camarines Sur), Viga (Catanduanes), Placer (Masbate) and Naujan (Mindoro) while T. laeviceps were found in Calapan (Mindoro), and Caramoan (Camarines Sur). For Visayas, the identified species were T. laeviceps in Hernani (Samar), Marbuena, and Nasidman (Iloilo) while T. sapiens in Tagbilaran (Bohol). In Mindanao, the species was identified as T. sapiens in Tagum (Davao). An unidentified species was found in Paniki (Aroroy, Masbate).
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