In this paper we describe a new apochelan species, Milnesium variefidum sp. nov. from Scotland and provide novel morphological and molecular data for Milnesium berladnicorum Ciobanu et al., 2014. The new species differs from the most similar M. berladnicorum by the presence of developmental dimorphism in claw configuration, absent or weakly developed cuticular bars under claws I-III, a different arrangement of cuticular pseudoplates, and by differences in the sequences of three nuclear DNA fragments: 18S rRNA (p-distance: 0.6%), 28S rRNA (2.0%), ITS-2 (9.3%), and on mitochondrial gene COI (12.4%). Although ontogenetic claw configuration change was suspected to occur in some Milnesium species, we are the first to document it through the combined use of traditional, molecular and experimental methodologies. We discuss the implications of the observed phenomenon for the taxonomy of the genus and propose a new diagnostic key to all Milnesium species described up to the end of 2015. We also review other traits used for species differentiation in the genus and offer recommendations to improve the quality of future descriptions as well as suggest a need for integrative redescriptions of the known species. Finally, we propose to suppress M. dujiangensis and M. tardigradum trispinosum and suggest that M. alpigenum and M. quadrifidum are valid species that require thorough redescriptions.