The assessment of biodiversity in coral reefs requires the application of geographic information systems (GIS), remote sensing and analytical tools in order to make cost-effective spatially explicit predictions of biodiversity over large geographic areas. Here we present a spatially explicit prediction for coral reef fish diversity index, as well as habitat classification according to reef fish diversity index values in Chinchorro Bank Biosphere Reserve, one of the most important plain/atoll type reef systems in the Caribbean. We have used extensive ecological data on depth, fish and habitat characteristics to perform such prediction. Fish species assemblages and different biotic variables of benthic organisms were characterized using visual censuses and video-transects, respectively at 119 sampling stations. The information was integrated in a GIS, along with satellite imagery (LANSDAT 7 ETM+) and a digital bathymetric model. From the recorded data and a hierarchical classification procedure, we obtained nine different classes of habitats. We used a generalized regression analysis and spatial prediction methodology to create predictive maps (GIS layers) of the different reef benthic components, and a second modeling run produced predictive maps of coral reef fish diversity index. Predictive accuracy of the diversity index map presented a good correlation coefficient ( r = 0.87), with maximum diversity index values en reefscapes composed of aggregation of coral colonies with seagrass beds. The implementation of our application was successful for the prediction of fish diversity hot spots and surrogate habitats.