Miocene crustose coralline algae (CCA) from Southeast Asia are poorly known, although the Miocene is the epoch of the onset of the biodiversity hotspot in the region and CCA are crucial to understanding the evolutionary history of reef building. To fill this knowledge gap, CCA from early and middle Miocene reefs and related carbonates in the Kutai Basin in East Kalimantan (Borneo, Indonesia) have been studied. The Kutai Basin was dominated by siliciclastic sediments of the proto-Mahakam Delta. Locally, carbonate buildups occur lateral to, or within, the deltaic succession. CCA in the Kutai Basin occur in carbonate beds that were deposited in a low-energy shallow-water platform setting and in association with coral reefs, encrusting the corals or bioclasts. Two main CCA assemblages are recognized herein: (1) a shallow-water assemblage (S-assemblage), dominated by Neogoniolithon spp., thick crusts of Spongites spp., and Hydrolithon spp.; and (2) the D-assemblage, which consists mainly of thin crusts of Lithothamnion spp., Mesophyllum spp., and Sporolithon spp., and is interpreted to have developed in darker waters. Light reduction in reefs in the proto-Mahakam Delta is interpreted to reflect either increased water depth or higher turbidity resulting from higher siliciclastic input. Assemblages with intermediate composition (I-assemblages) also occur. Common CCA with large cell fusions and groups of heterocysts, typical features of modern reef CCA, in the S-assemblages in the middle Miocene of East Kalimantan reflect the initiation of the reef-building CCA flora in the Indo-Pacific region. The occurrence of this kind of CCA confirms the biogeographic differentiation of a tropical reef flora.