The minute aquatic beetle genus Notomicrus Sharp (Coleoptera: Noteridae) is most diverse in the Neotropics, with significantly more species and greater ecological variation than in the Old World. Investigation of Neotropical Notomicrus has recovered well-structured relationships and diagnosable traits among most Neotropical species. The exception to that is within the N. traili complex, in which interspecific variation is subtle and geographic patterns difficult to parse. Using a tailored, noterid-specific, ultraconserved element probeset, we captured phylogenomic data from 45 ingroup samples from across the N. traili complex, with recovered datasets surpassing one thousand loci. We will use these data to (1) successfully infer species- and population-level relationships, (2) delimit lineages to guide taxonomy within the group, and (3) investigate the biogeographic history of the complex. We show that the N. traili complex includes multiple distinct lineages and within these, we recover a historical pattern consistent with repeated episodes of diversification and range expansion in South America. Data recovery metrics, phylogenetic estimates, and results of preliminary phylogenetic reconstructions are reported and discussed.