Novel implications for the basal internal relationships of Gastrotricha revealed by an analysis of morphological characters. -Zoologica Scripta , 37 , 429-460. A cladistic analysis of Gastrotricha based on morphological characters is presented. Unlike previous morphological analyses, our study uses species rather than higher level taxa, for which the ground pattern is often unknown. The analysis comprises 79 ingroup taxa, 4 outgroup taxa and 135 binary and multistate characters in total. Character coding is based on a careful assessment of original species descriptions. Characters included cover general body organization, internal and external features as, for example, data on the adhesive tubes, digestive tract or cuticle armament. Character systems such as many ultrastructural findings, for which it was problematic to obtain data for a large set of the included taxa, were not considered. To minimize a priori assumptions, all characters were treated with equal weight and left unordered. The four outgroup representatives were chosen in accordance with the current sister group hypotheses for Gastrotricha. Two search strategies, a heuristic search (maximum parsimony) and a parsimony ratchet search, reveal a comparable scenario. Gastrotricha split into two sister taxa. One group comprises genus Neodasys only, the sister group N.N.1 (Eutubulata nom. nov.) consists of all remaining Gastrotricha. Within Eutubulata, monophyletic Macrodasyida s. str. and N.N.2 (Abursata nom. nov.) are sister taxa of highest rank. Abursata consists of the 'freshwater macrodasyids' Marinellina and Redudasys as sister group of monophyletic Paucitubulatina. Some traditional families are supported by this analysis. We evaluate possible apomorphies for the most basal stem lineages and track the evolution of selected organs. Our findings reveal that secondary character loss may play an important role in the stem lineage of Abursata and further in Paucitubulatina. Moreover, according to this analysis there might have been a single invasion of the freshwater environment in the stem lineage of Abursata followed by several independent returns to marine habitats within the monophylum Paucitubulatina.