Gastrotricha is a cosmopolitan group ofaquatic invertebrates. To date, approximately 765species have been described. This study is the first todeal with species delimitation and cryptic species offreshwater Gastrotricha. Three commonly encounteredspecies, Heterolepidoderma ocellatum, Lepidochaetuszelinkai, and Lepidodermella squamata, areinvestigated for cryptic speciation. Most of thematerial is based on Swedish specimens but closelyrelated species from other parts of the world are alsoincluded. Taxonomic revisions are supported byphylogenies based on 18S rRNA, 28S rRNA, andCOI mtDNA of freshwater Chaetonotidae from severalgenera and inferred from Bayesian and maximumlikelihood approaches. Heterolepidoderma ocellatumf. sphagnophilum is raised to species level, under thename H. acidophilum n. sp. Moreover, genetic databased on COI indicate large variation between twomorphologically very similar groups of Lepidodermellasquamata. The extent of cryptic speciation inL. zelinkai appears low. Based on the phylogenetichypothesis presented in this article, the new species,Lepidodermella intermedia n. sp., from northernSweden is also described. The phylogenetic hypothesisgenerated shows that Chaetonotidae is a nonmonophyleticgroup