The present study aimed to identify the preferential habitats of spiny lobster ( Panulirus argus) and associate its density, abundance and biomass to each type of habitat, enable hence prediction of the spatial distribution of the crustacean in the whole area. It also attempted to identify the associated size population structure at different areas of the reef. To do so, a study was undertaken at the National Park “Arrecife Alacranes” in Yucatan, Mexico. First, with the use of geographical information systems (GIS) tools, a thematic map of submerged habitats (bottom type) of the reef area was overlaid to lobster distribution data obtained from 157 diving transects in order to estimate lobster density, abundance and biomass by bottom type. Uncertainty of the analyzed variables was incorporated through Monte Carlo simulation. In addition, the spatial structure of lobster habitat was predicted by using geostatistical tools (kriging) to estimate lobster density from 420 stations sampled by diving in the same reef. Population size structure was obtained from catch data obtained from fishers’ landings and based on records of small individual juveniles collected by fishers. The results show a patchy distribution of lobsters throughout the entire reef, with higher densities predicted in areas of higher habitat complexity. This study supports thus the thesis that structural complexity of habitat has an influence on lobster spatial distribution and emphasizes the relevance of undertaking spatial analysis to study lobster populations.