We examine inter- and infrageneric relationships of the stingless bees with a near complete sampling of supra-specific taxa. DNA sequences for the taxa were collected from five genes (mitochondrial 16S rRNA, nuclear long-wavelength rhodopsin copy 1 (opsin), elongation factor-1α copy F2 (EF-1α), arginine kinase (ArgK) and 28S rDNA). Results indicates that Trigona s.l. is not monophyletic: Trigona from the Indo-Malay/Australasian Regions forms a large clade distantly related to the Neotropical Trigona. A separate clade comprises the Afrotropical meliponines, and includes the “minute” species found in the Afrotropical, Indo-Malayan, and Australasian Regions. We then explore a subset of our data, 24 species of Trigona s.str., and codify 15 nest related characteristics and test them for a phylogenetic association. We report several characters with significant phylogenetic signal within Trigona s.str., including the nesting substrate and the construction of exposed nests, nest construction material, hemiterophily, while we discuss particular habits encountered in Trigona s.str., including the evolutionary labile traits of coprophily and necrophagy.