This project reviewed the functional and evolutionary ecology of wild bee microbiota - focusing on the bee tribe Allodapini, where natural history and behavioural ecology is well known but investigations of microbiology are just beginning. Opportunities to improve our future knowledge of pathogens to insect pollinators were explored – which have broad ramifications for crop pollination services, considering the current overdependence on a few managed species that face a multitude of health threats. The ability to parse intrinsic and extrinsic factors influencing microbiome patterns within and between species means that allodapine bees provide the opportunity for an integrated approach to bee socio-eco-evo-immunology. This archived dataset provides aligned nucleotide sequences of small subunit ribosomal ribonucleic acid (SSU rRNA) genes from four groups of microbial associates of allodpine bees derived from published genomes of species from the genera Exoneura and Exoneurella. Alignments of gene sequences were used to construct molecular phylogenies of common bee cobionts, namely: (A) Commensalibacter sp.; (B) Sodalis sp.; (C) Microsporidia; (D) Gregarines. Phylogenetic trees are presented in Figure 3 of the published Evolutionary Applications article. Results enabled discovery of novel microsporidian and protozoan parasites and relatives of known bee bacteria (Commensalibacter, Sodalis). This dataset contains Nexus files [.nex] of nucleotide sequence alignments of small subunit ribosomal ribonucleic acid (SSU rRNA) genes: - Commensalibacter_alignment.nex - Gregarine_alignment.nex - Microsporidia_alignment.nex - Sodalis_alignment.nex