The Antillean manatee Trichechus manatus manatus is considered endangered because of its reduced numbers, poor knowledge about its population status, and human modification of rivers, estuaries and coastal areas which it inhabits. Previous studies identified some elements of the habitat of manatees in the Caribbean, but few have explored quantitatively their relationship with their use by manatees, specially at a local scale. We explored the correlations between several habitat characteristics and the use of small spatial units by manatees in Bahia de Chetumal. Distance to freshwater sources, vegetation cover, depth, slope, salinity and shelter were sampled concurrently during 17 manatee aerial surveys, between November of 1998 and April of 2000. All variables, except shelter, were correlated with the occurrence of manatees. The distance to freshwater and depth contributed the most to multivariate Poisson and Logistic regression models and should be considered first in developing habitat models and conservation strategies for this species.