Modern single chambered monothalamids are largely understudied representatives of early-evolving foraminifera despite their widespread presence in marine, freshwater, brackish and even terrestrial habitats. Unlike polythalamids, taphonomic vulnerability, lack of a consistent fossil record and their simple gross morphology makes evolutionary affinities difficult to elucidate. Of thirteen clades delineated by small subunit ribosomal DNA (SSU rDNA) phylogenetics, the Clade E lineage is composed of taxa that do not share a common general morphology but appear to have a loose molecular affinity. Membership of taxa suspected to be in Clade E was tested using Bayesian statistics on the SSU rDNA gene and by multiple genes (SSU rDNA, actin, -tubulin). Both methods returned a core group (Psammophaga spp., Xiphophaga spp., Vellaria spp.) identified as Clade E whereas remaining taxa are excluded from the clade. Relationships among orphan taxa cannot be determined without an increase in taxon sampling. The multi-gene analysis shifted relationships in the SSU rDNA based tree without an increase in node support.Ultrastructural data show a consistent architectural theme among all evalutated taxa regardless of phylogenetic placement. All possess an electron-transparent inner organic lining (IOL) containing electron-dense fibers and granules. The IOL is in direct contact with the plasma membrane and test construction materials are released into the IOL exocytotically or by direct transfer via vesicles. All taxa possessed a single nucleus and cytoplasmic stercomata found in some deposit-feeding foraminifera were observed in two. Overall shape, thickness, mineralogic composition and packing of the agglutinated layer, and IOL thickness varied among all taxa and did not correlate with placement in phylogenetic trees. Variability in gross morphology of closely related monothalamids is taxonomically uninformative. Conversely, wall ultrastructure appears to be consistent among the core Clade E and the orphan taxa that cannot be placed into any particular clade at this time. These orphan taxa appear to be close relatives of Clade E based on wall ultrastructure but cannot be considered true members through phylogenetics. Increased taxonomic sampling of monothalamids is required to improve phylogenetic signal in molecular trees and further delineate potential evolutionary patterns of ultrastructural features.