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The rare minnow <i>Gobiocypris rarus</i> is an ideal model organism for toxicological research. <i>Dactylogyrus</i> species are usually found on the gills of this rare minnow in laboratory farming systems. Dactylogyrid infection may change the sensibility of fish to toxicants and affect toxicological evaluations. In the present study, dactylogyrid infection was investigated, and species of <i>Dactylogyrus</i> collected from rare minnows were determined. Based on the observed ‘<i>D. wunderi</i>’ type anchors, with a shorter outer root and elongated inner root, and accessory piece consisting of two parts, the dactylogyrids were identified as <i>D. gobiocypris</i>. A partial 18S-ITS1 rDNA sequence was firstly sequenced, and the highest sequence identity (86.7%) was to <i>D. cryptomeres</i>. Phylogenetic analysis revealed that <i>D. gobiocypris</i> formed a clade with <i>D. squameus</i>, <i>D. finitimus</i>, and <i>D. cryptomeres</i>, all of which have been recorded in the family Gobionidae. Histopathology analysis indicated that a heavy burden of <i>D. gobiocypris</i> caused necrosis of gill filaments. Inflammatory responses, such as tumefaction and hyperaemia, were also observed on gills with severe dactylogyrid infection. Supplementary morphological characteristics and 18S-ITS1 rDNA sequence provided basic data for identification of this parasite species.