To establish the biogeographic affinities of the caddisfly fauna of Mongolia, published records and results of our faunistic studies were analyzed. This study captured more than 47,000 adults collected from 386 locations beside lakes, ponds, streams/rivers, and springs in ten sub-basins of Mongolia using Malaise traps, aerial sweeping, and ultraviolet lights. In total, 201 species have been recorded, and approximately 269 species may occur in Mongolia according to our estimation. In a comparison of species richness for the family level, the Limnephilidae and Leptoceridae were the richest in species. The families Brachycentridae, Glossosomatidae, and Psychomyiidae had low species richness, but they included the most dominant species in terms of abundance and/or the percentage of occurrence in the samples from multiple sub-basins. Comparing the sub-basins, the Selenge had the highest Shannon diversity (H' = 3.3) and the Gobi sub-basin had the lowest (H' = 1.5). According to the Jaccard index of similarity, caddisfly species assemblages of Mongolia's ten sub-basins were divided into two main groups: One group includes the Selenge, Shishkhed, Bulgan, Tes, and Depression of Great Lakes sub-basins; the other group includes the Kherlen, Onon, Khalkh Gol, Valley of Lakes, and Gobi sub-basins. The majority of Mongolian species were composed of East Palearctic taxa, with a small percentage of West Palearctic and Nearctic representatives and an even smaller percentage from the Oriental region, suggesting that the Mongolian Gobi Desert is, and has been, a significant barrier to the distribution of caddisfly species between China and Mongolia.