Blind snakes (Typhlopidae) are an enigmatic group of small burrowing snakes whose anatomy, phylogenetics, and biodiversity remain poorly known. Madatyphlops comorensis (Boulenger, 1889), endemic to the Comoros Archipelago in the Western Indian Ocean, is one of many species whose phylogenetic placement and generic assignment is unclear. We used DNA barcoding, external morphological examination, and osteological data from 3D reconstruction with micro-CT to study specimens of Madatyphlops from the Comoros Archipelago. Our results support the placement of M. comorensis in Madatyphlops and the recognition of the specimens from Mayotte Island as a closely related but distinct species, which we describe as Madatyphlops eudelini sp. nov. In this context, we present the first detailed osteological descriptions of any species of Madatyphlops, which we hope will serve as groundwork for further osteological studies in this genus and contribute to our limited but growing understanding of the osteology of typhlopid snakes.