Crustose coralline algae (CCA) play a key role in calcification and consolidation of substrate on coral reefs, with some species also providing important settlement substrate for coral recruits. Like corals, CCA suffer diseases that threatens their survival and persistence (Vargas-Ángel 2010), including a fungal disease that results in rapid tissue necrosis, particularly during ocean warming events (Williams et al. 2014). Coralline fungal disease (CFD) was first reported at the island of Tutuila in American Samoa in 1998 (Littler and Littler 1998) and later at the islands of Swains and Rose in American Samoa (Vargas-Ángel 2010). Other reports of CFD are restricted to the remote central Pacific at Kingman Reef and Palmyra Atoll in the northern Line Islands (Vargas-Ángel 2010; Williams et al. 2014). Here we report on the first field sightings of CFD in the Indian Ocean at islands within the remote and highly protected Chagos Archipelago, British Indian Ocean Territory (Fig. 1). Of the 29 reefs surveyed during an expedition in April 2018 across ~ 200 km of latitude, CFD was documented at 8 of them. CFD sightings were restricted to shallow (< 15 m depth) fore reef habitats and not observed on backreef or patch reef habitats. At two reefs, CFD was at outbreak levels, with > 5 cases m−2 of CCA. These are among the highest densities of CFD ever reported and appeared to correlate with high host density at these locations (> 50% host CCA cover). The coral reefs of the Chagos Archipelago suffered from back-to-back ocean warming events in 2015, 2016 and 2017 that have reduced live hard coral cover. The high densities of CFD recorded here may represent a residual impact of these warming events but whether CFD significantly alters key reef processes such as accretion, coral recruitment and substrate consolidation across the region requires further study.