The colorless amoeboid eukaryote genus Leukarachnion represents one of a long list of microbial lineages for which there have been few taxonomic studies. In this study, we analyze molecular data to assess the placement of a species of Leukarachnion on the eukaryotic tree of life and we report fine structural data to provide additional information on the identity of this taxon. Our multigene analyses indicate that Leukarachnion sp. (ATCC PRA-24) is a member of the stramenopiles, sister to the Chrysophyceae/Synurophyceae clade. It also forms a sister group relationship to the clade containing Chlamydomyxa labyrinthuloides and Synchroma grande, both of which are characterized by net-like amoeboid phases. Leukarachnion sp. and Chlamydomyxa labyrinthuloides also share fine structural cyst morphology such as bilayered structure of the cyst wall. The amoeboid form and heterotrophic habit of Leukarachnion sp. highlight the multiple origins of diverse body forms and multiple plastid losses within the stramenopiles.