AbstractEuglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being most elusive. Ploeotids make up most of this backbone diversity—yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show that they are non‐monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships amongst these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single‐cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater‐dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon.