Abstract The present study aimed to reveal the microbial (bacteria and yeast) composition of raw milk from dairy camel (n = 10), cow (n = 10) and goat (n = 10) in North-western Nigeria. High-throughput DNA metabarcoding was used to compare microbial compositions in raw milk among the three species. Although the three species had similar dominant bacterial (Firmicutes and Proteobacteria) and yeast (Ascomycota and Basidiomycota) phyla, their microbial compositions at the genus level were noticeably different. The top differentially abundant bacterial and yeast genera (percentage abundance) were Lactobacillus (36%), Streptococcus (34%), Enterococcus (12%), Kluyveromyces (28%), Saccharomyces (24%), and Candida (18%), respectively. Principal coordinate analysis based on unweighted UniFrac values revealed significant differences in the structure of bacterial communities and no differences in yeast communities in milk samples from the three species. This study provides insight into the rich and diverse bacterial and yeast communities in raw animal milk consumed in Nigeria, which could play beneficial roles or pose health threats to consumers. However, further research on the economic significance of the microbial community in animal milk consumed in Nigeria is required.