The Arctic, despite being profoundly affected by global climate change, remains largely understudied. Its local ecosystems and fauna are undergoing significant changes, including marine meiobenthic invertebrates, such as kinorhynchs. However, although they are an important component of the benthic meiofauna, our understanding of their communities remains relatively limited. The present study focuses on the structure and connectivity of the populations of three Echinoderes species: Echinoderes aquilonius, E. eximus and E. remanei, inhabiting the coastal area of Disko Island (Western Greenland). A hypothesis of low population diversity was tested through analyses based on both morphology and the molecular cox1 marker. For the first time the distribution and relationships between and within species were described. Phylogenetic analysis and haplotype networks reflected the results of population statistics (nucleotide and haplotype diversity, Tajima’s D and Fu’s Fs), revealing expected homogeneity and low diversity, without any noticeable patterns of geographical distribution. The results indicate that Arctic kinorhynchs form progressively developing and expanding communities. Additionally, the analyses revealed a taxonomically important example of intraspecific polymorphism. Presence or absence of tubes are usually considered to be species diagnostic characters, and the finding an isolated population of E. eximus-like specimens with sublateral tubes on segment 9, suggested that this could be a new, yet undescribed species. However, the genetic divergence between these specimens and other populations of E. eximus without tubes on segment 9 was so low that they all have to be considered conspecific. This is the first time molecular sequence data has provided evidence for intraspecific tube polymorphism among kinorhynchs.