Reefal microbial crusts (RMCs) are fine-grained, non-skeletal carbonate crusts coating coralgal reef frameworks, and are locally common in late Quaternary reef deposits. They are interpreted as microbial carbonates produced by the growth and metabolism of benthic bacterial communities. Key questions remain concerning their uneven spatio-temporal distributions, formation process and controlling factors; the crusts have not yet been reported in the Ryukyu Archipelago. Here we report the first occurrence of brownish, few-centimeter-thick, fine-grained, non-skeletal crusts in a Middle Holocene reef core recovered at Naha New Port Pier, off the western coast of Okinawa Island, the Ryukyu Archipelago. The outer morphology of the crusts is either knobby or flat. The meso-scale fabric of the crusts is generally clotted and structureless, while a few crusts are weakly laminated or digitate. The slab core shows a biological succession from a bioeroded coral oriented upward, overlain by thin crusts of coralline algae and encrusting foraminifers, ending in a brownish, fine-grained, non-skeletal crust. Surface elemental mapping shows that the crusts are composed mainly of Ca and Mg (i.e., Mg-containing carbonate). X-ray diffraction analysis indicates that the crusts are composed predominantly of high-magnesium calcite, subordinate with aragonite and quartz. Petrographic observations show that the crusts are made mainly of peloidal micrite with irregular voids (cavities), associated with silt-sized bioclastic and siliciclastic grains. The crusts develop within a particular core depth and age range (4.6-6.1m depth; ca. 7ka), from which the crusts change downward and upward into encrusting bryozoan and foraminiferal crusts filled with micrite. Based on our observations, compared with previous studies, we conclude that brownish, non-skeletal carbonate crusts found in this study are RMCs, similar to those found in the last glacial, last deglacial and Holocene reef deposits from other coral reef regions (e.g., Tahiti and Great Barrier Reef). The RMCs likely developed in a low light/darker, semi-enclosed environment within primary cavities of high-energy, shallow-water coralgal frameworks. Since the study area is located adjacent to a river mouth and directly exposed to terrigenous sediment input from river runoff, multiple, local and global environmental factors associated with Holocene transgression and reef formation likely influenced the development of RMCs in the study area.