The chicozapote (Manilkara zapota) is a tropical fruit tree that occurs in two morphologically distinct populations in the Yucatan peninsula of Mexico. Forest populations consist of tall, straight trees, while swamp populations have a short, shrub-like growth form. Swamp populations also have smaller leaves, fruit and seeds. We performed a random amplified polymorphic DNA (RAPD) analysis on four different populations of chicozapote to test if there was a genetic component to this variation. The populations differed in respect to habitat type (swamp vs. forest) and geographical location (east vs. west). We surveyed 80 random primers, nine of which revealed interpopulation band differences (28 band differences in total). Unweighted pair group method analysis (UPGMA) and neighbour-joining dendrograms showed no separation of individuals between the different populations. Analysis of the RAPD data showed no significant differences between swamp and forest populations (P > 0.1). The lack of genetic differentiation suggests a failure to find a correlation between the RAPD loci and adaptive traits. The observed morphological differences between the swamp and forest populations of chicozapote may either be that gene flow has prevented a build-up of neutral marker differences or a plastic response to differences in habitat.