A phylogenomic study of neglected flagellated protists supports a revised eukaryotic tree of life. The research analyzed 22 newly sequenced transcriptomes of early-branching protists, including apusomonads, ancyromonads, and Meteora, to better understand their evolutionary relationships. The results support the monophyly of Opimoda, a major eukaryotic supergroup, with CRuMs as sister to Amorphea. The study also reveals that the ancestor of Opimoda was a biflagellate with an excavate-like feeding groove. Breviates and apusomonads retained the ancestral biflagellate state, while other Amorphea lineages lost one or both flagella, enabling the evolution of amoeboid shapes, novel feeding modes, and palintomic cell division, which likely facilitated the evolution of fungal and metazoan multicellularity. The study highlights the importance of incorporating diverse and underrepresented lineages in phylogenetic analyses to resolve the eukaryotic tree. The results suggest that the last common ancestor of Opimoda had a biflagellate, excavate-like phenotype, and that the eukaryotic tree is likely rooted in a common ancestor with a complex cytoskeleton and flagellar apparatus. The study also identifies new molecular synapomorphies and provides insights into the evolution of major phenotypic traits during the early eukaryotic radiation. The findings contribute to a more accurate understanding of eukaryotic diversity and evolution.A phylogenomic study of neglected flagellated protists supports a revised eukaryotic tree of life. The research analyzed 22 newly sequenced transcriptomes of early-branching protists, including apusomonads, ancyromonads, and Meteora, to better understand their evolutionary relationships. The results support the monophyly of Opimoda, a major eukaryotic supergroup, with CRuMs as sister to Amorphea. The study also reveals that the ancestor of Opimoda was a biflagellate with an excavate-like feeding groove. Breviates and apusomonads retained the ancestral biflagellate state, while other Amorphea lineages lost one or both flagella, enabling the evolution of amoeboid shapes, novel feeding modes, and palintomic cell division, which likely facilitated the evolution of fungal and metazoan multicellularity. The study highlights the importance of incorporating diverse and underrepresented lineages in phylogenetic analyses to resolve the eukaryotic tree. The results suggest that the last common ancestor of Opimoda had a biflagellate, excavate-like phenotype, and that the eukaryotic tree is likely rooted in a common ancestor with a complex cytoskeleton and flagellar apparatus. The study also identifies new molecular synapomorphies and provides insights into the evolution of major phenotypic traits during the early eukaryotic radiation. The findings contribute to a more accurate understanding of eukaryotic diversity and evolution.