We evaluated the distribution and the extent of sea-spawning whitefish Coregonus lavaretus (L.) s.l. and vendace Coregonus albula larval areas in the Gulf of Bothnia, northern Baltic Sea, and suggest that the distribution of the reproduction areas could be an indicator of the health of the Baltic Sea shores. Our Geographic Information System (GIS) based predictive spatial model of habitat selection covers nearly the whole distribution area of both species. Extensive sampling data on larval occurrence were combined with GIS raster layers on environmental variables and used in a Gaussian process model, which predicts the spatial probability of larval occurrence. Out of 22 studied variables, shore profile, distance to sandy shallow shore, distance to 20 m depth contour line and ice break-up week were the most important for describing larval areas of both species. The earliest larval stages of sea-spawning whitefish can be found in various habitats close to the shoreline, but the highest densities of larvae were observed along gently sloping, shallow sandy shores. Vendace reproduction occurs in the northernmost and less saline areas of the Bothnian Bay and larval stages use the shallow areas. Compared to previous studies from 1990s, the extent of whitefish larval areas has decreased. We discuss the possibility that long-term changes in the environment, such as more frequent iceless winters and increasing eutrophication, have reduced the reproductive success of sea-spawning coregonids. Larval distribution maps can be used to focus conservation measures in the most appropriate places. We propose to use this method as a monitoring tool, and produce maps to assist integrated coastal zone management and environmental protection