Here we used targeted sequence capture of ultra-conserved elements (UCEs) to generate a phylogenomic dataset for estimation of schistosome interrelationships. This dataset represents the largest phylogenetic effort within Schistosomatidae in both the number of loci and breadth of taxon sampling. We present a near comprehensive family level phylogeny providing resolution to several long-standing clades within Schistosomatidae, including resolution of the placement of the North American mammalian schistosomes, supporting a secondary host-capture of mammals.