Sainouroidea, is a clade of protists that belongs to the eukaryotic assemblage Rhizaria. Sainouroidids exhibit remarkable genetic and phenotypic heterogeneity. Members can be flagellates or amoeboid organisms; some are strictly unicellular, while others can be facultatively multicellular, and one member even has an alternative nuclear genetic code. Sainouroidids can be found in marine, freshwater, and terrestrial environments, as well as the gut contents and feces of various animals. A well-resolved phylogeny and data from non-primer biased eDNA studies are crucial first steps in developing hypotheses regarding the evolutionary history of diverse traits and lifestyles exhibited by sainouroidids. The small subunit ribosomal RNA (SSU RNA) gene is the most used single gene marker for molecular phylogenetic and amplicon-based eDNA studies in protists. However, the exact phylogenetic placement of Sainouroidea within Rhizaria as well as their presence in diverse environments is obscured by the highly divergent nature of this marker in members of this clade. To date, multigene phylogenies have done little to resolve this issue due to limited genomic data from sainouroidids and close relatives. To help resolve the position of sainouroidea within Rhizaria as well as the internal relationships between members of the group, we generated novel transcriptomic data from five sainouroidid taxa. We use these data to perform multigene phylogenomic analyses of Rhizaria, including Sainouroidea. Additionally, to better understand the ecological niche range and genetic diversity of sainouroidids we query publicly available meta “omic” datasets using the recently developed tool NCBI tool “PebbleScout” for the presence of diverse sainouroidids.