In Japan, the subtropical Ryukyu Archipelago (RYS; also known as the Nansei Islands) with its coral reefs has been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of scientific literature in the Web of Science (WoS; 1995-2017) on six selected representative taxa spanning from protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate the clear need to study ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), and to study ‘understudied areas’ of some sub-regions away from marine research stations. Second, we compared the numbers of scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAB), Great Barrier Reef (GBR), and the Red Sea (RES). Not unexpectedly, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on ‘marine protected areas’ and ‘herbivory’ was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAB, RES, and GBR (4.6 to 8.4 times). As the RYS are considered to contain among the most critically endangered coral reef biodiversity in the world due to high levels of both endemism and anthropogenic threats, much work is urgently needed to address the areas of relative research weakness identified in this study.