Garra gotyla is a benthopelagic freshwater cyprinid fish native to Asia, valued for both food and ornamental purposes; nevertheless, its parasitic diseases are poorly understood. The present study investigated the presence and ecological indices (prevalence and intensity) of monogenean parasites infecting G. gotyla in Mizoram, northeast India. Additionally, the study aimed to assess the phylogenetic relationships among three closely related dactylogyrid genera: Dactylogyrus, Dogielius, and Dactylogyroides. Monogeneans were initially identified based on the comparative morphology of their sclerotised haptoral and reproductive structures, followed by BLASTn comparisons of their partial 28S rRNA gene sequences. Two dactylogyrid species, Dactylogyrus labro sp. n. and Dogielius salpinx sp. n., were recovered and are described herein as new to science. Dactylogyrus labro was found to infect all examined fish, whereas D. salpinx had a slightly lower prevalence, ranging from 76.5% to 83.3% across different sampling sites. The phylogenetic insights from these species presented in this study highlight the complex evolutionary relationships within these three genera. Further, this study provides the first confirmed molecular data for a Dogielius species, allowing for much-needed phylogenetic studies on the genus and filling a gap in sequencing data for Indian monogeneans. Since all monogeneans are potentially hazardous parasites, more studies are needed to map their diversity and effects on host fishes in this region.