Miocene bryozoans from the Indonesian Archipelago have seldom been investigated in the past. Several factors combine to explain their poor fossil record, including rare exposures in a lushly vegetated terrane, dominance of inconspicuous encrusting species, and the adverse effects of diagenesis on fossil preservation. A large collection of samples from the Kutai Basin (East Kalimantan) has allowed new insights into the diversity of Miocene bryozoans in this region. The bryozoan assemblage as a whole consists of 123 species; a remarkable increase in known diversity. Substrate availability appears to be the main factor controlling bryozoan distribution. The majority of encrusting species are associated with plate-like scleractinian corals. Collecting curves allow sampled sites to be divided into three groups characterized by high, medium, and low species richness. The site of highest diversity is a mesophotic reef slope, an environment influenced by high input of terrigenous sediment. Ordination plots show no clear patterns of distribution among sites, with putatively endemic species accounting for most of the discrimination. A similar level of endemism and habitat heterogeneity characterizes modern, tropical bryozoan faunas. However, many more intermediate sites need to be sampled to achieve a fuller understanding of the true pattern of bryozoan species distribution in the Miocene of the Kutai Basin.