Polymetallic nodule fields represent a large reservoir of undiscovered biodiversity that becomes particularly evident for meiobenthic organisms, the smallest-sized faunal group. Knowledge gaps are especially noticeable for the generally low-density metazoan groups, such as Kinorhyncha, the so-called mud dragons. Using both morphological and genetic (metabarcoding) approaches, we provide a general overview and comparison of the diversity of kinorhynchs collected during nine sampling campaigns (2016–2019) that targeted abyssal environments in several contract areas for exploration in the Clarion-Clipperton Fracture Zone (CCZ) and in the Peru Basin. Our findings from morphological analyses reveal a highly diverse mud dragon community, with 16 species present in the CCZ. Of these, 12 appear in the German contract area, including three new species described in the present contribution: Echinoderes delaordeni sp. nov., Echinoderes sanctorum sp. nov., and Echinoderes zeppilliae sp. nov. Furthermore, metabarcoding data of the kinorhynch community gathered from the area is provided, together with the geographic distribution of the known species stated per contractor area, including new records and still undescribed species. Most of the identified species in the CCZ seem to have a wide distribution, with Echinoderes sp.4 being the most common and abundant species with a distribution spreading across the CCZ and also present in the Peru Basin. Metabarcoding analyses targeting the V1V2 hypervariable region of the 18S gene from the 253 stations of the CCZ revealed 14 amplicon sequence variants (ASVs) belonging to Kinorhyncha with grade values higher than 98% detected at 15 different stations within six different areas along the CCZ. Concurring with morphology, the family Echinoderidae was the most diverse as the genus Cephalorhyncha had five ASVs, followed by Echinoderes with four ASVs. Semnoderes, however, showed the widest spread ASV, being detected at six stations. In the CCZ, the metabarcoding data showed there were no shared ASVs between the CCZ areas as well as the highest number of uniques, which was 11. Our morphological study showed a low number of specimens inhabiting nodules (surface/crevices), suggesting that specific kinorhynch species do not typically inhabit the nodules in addition to the surrounding sediment.