The forces that drive population divergence and speciation in sexually reproducing organisms have long been debated with contributions from both theoretical and empirical data. Studies of genetic and phenotypic characters of previously isolated populations that meet in secondary contact provide one method of investigating these forces. In this study, multivariate techniques were used to analyse quantitative trait variation and dewlap hue variation in Anolis roquet along two geographically proximate and parallel transect in different habitats on the island of Martinique. Diagnostic PCR-RFLP was used to assign individuals to lineage. Nuclear DNA microsatellites were developed and employed for population genetic screening along the transects, and for the study of sex-biased dispersal. Microsatellite data were analysed using traditional summary statistics and Bayesian assignment analysis. These methods were further complemented with the modeling of diagnostic mtDNA markers, nuclear microsatellite markers, quantitative trait variation and dewlap hue variation with cline fitting techniques. Results from quantitative traits, dewlap hue data and microsatellite data suggested that barriers to gene flow in accordance with an allopatric model of speciation existed on a coastal transect, and that these barriers were maintained by a balance between selection and dispersal. Moreover, potential for assortative mating and selective advantage of dewlap hue were determined for the coastal transect. In contrast, quantitative traits, dewlap hue data and microsatellite data suggested that there were no barriers to gene flow on a transect in transitional forest habitat, in spite of the close proximity of the transects and their shared geological history. Patterns of geographic variation on these two transects, together with environmental data, suggest that selection regimes on either side of the secondary contact zone in the transitional forest may be more convergent, while those either side of the secondary contact zone on the coast are more divergent. Secondary contact dynamics between previously isolated populations of A. roquet are therefore highly contingent on local natural selection pressure, and allopatry may play a role in the diversification of Anolis lineages, subject to selection pressures. Sex-biased dispersal is common in sexually reproducing species, and has been widely documented in mammals and birds. Male-biased dispersal was tested in A. roquet using microsatellite data, and found to be highly significant. This finding was in accordance with predictions from the polygynous mating system of A. roquet, and agrees with similar results from an other species of anole. The finding of male-biased dispersal also goes some way to explaining the contrasting geographical patterns of maternal and biparental markers observed in A. roquet. The implications of this work is discussed in relation to diversification of Lesser and Greater Antillean anoles, secondary contact zones of similar organisms and current views on the mechanism of speciation.