Hyperamoeba dachnaya, a new taxon affiliated with Hyperamoeba flagellata, is described from freshwater anaerobic sediments. Organisms exist as amoeboid flagellates, amoebae and cysts. The flagellates of H. dachnaya are distinguished from those of H. flagellata by larger size and a longer anteriorly-directed finger-shaped pseudopodium. H. dachnaya cysts have bilaminar walls with connectives between the outer and inner layers appearing to be T-shaped spines, while cyst walls of H. flagellata are smooth. H. dachnaya has two basal bodies and a single anteriorly-directed flagellum emerging from the anterior one (BB1). A fibrillar rootlet with a microtubule organising centre (MTOC;'R1') arises from a diaphragm-shaped basal plate at the base of BB1; a short striated fibre (SSF) covers the dorsal side of BB1 and initiates microtubular rootlets 'R2' and 'R3' and the fibrillar bridge leading to microtubular rootlet 'R4'. 'R5' is composed of 2 microtubules splitting from R4 and 2 others initiating by BB1. The posterior basal body is associated with a fibrillar posterior parakinetosomal structure. A long striated fibre arises in association with the right end of the SSF. A Golgi apparatus is associated with the flagellar apparatus.The flagellar apparatus is present internally in amoebae. All three stages have mitochondria with tubular cristae and an electron-dense central body. Analysis of small subunit ribosomal RNA sequences shows H. dachnaya branching with the myxogastrids within the mycetozoa, but polyphyletic with a nominal Hyperamoeba sp. isolate that is morphologically similar to H. flagellata. We reject the suggestion that H. flagellata and this Hyperamoeba sp. isolate of Zaman et al. (1999) are conspecific. The study reveals extensive similarities between Hyperamoeba and the flagellated stages of myxogastrids.