Mange mites are obligate ectoparasites of horses and are responsible for significant skin disease, yet their detection in equine faecal samples remains largely unreported. During a routine coprological survey of horses attending a polo tournament in Ibadan, Nigeria, oval structures inconsistent with known equine helminth eggs were unexpectedly observed in a proportion of faecal samples. This study aimed to determine the prevalence of mite eggs in faecal samples from horses originating from six states in Nigeria, evaluate associations with host-related factors, and perform molecular characterisation of selected positive samples for species-level identification. Faecal samples from 167 horses were examined using the zinc sulphate flotation concentration method. Mite egg-positive samples were identified morphologically, and two randomly selected positive samples were subjected to PCR amplification of the 18S ribosomal RNA gene and Sanger sequencing for molecular identification. Mite eggs were detected in 39 horses (23.35%). State of origin was the only factor significantly associated with prevalence (p = 0.041), with Lagos (30.00%) and Ibadan (26.15%) recording the highest rates. No significant associations were found with breed, sex, or age group. Molecular analysis identified Chorioptes bovis and Psoroptes ovis, representing the first molecular confirmation of these species in Nigerian equines. These findings highlight the importance of training laboratory personnel to recognise mite eggs as incidental but diagnostically significant findings during routine faecal parasitological examinations, given their morphological similarity to certain helminth eggs. Concurrent skin examination and expanded molecular surveillance are recommended in future studies.