The Muridae rodent community of Guadeloupe and Martinique (French West Indies) includes 3 alien species: the Ship Rat (Rattus rattus), the Norwegian Rat (Rattus norvegicus) and the House Mouse (Mus musculus). A 26,740 trap-night effort conducted under standardized sampling methods showed a strong heterogeneity of the species frequency distribution among 4 agricultural ecosystems (sugar cane, banana, cassava and watermelon) and 3 "natural" ones (tropical rain forest and islands or islets covered either totally or partially by a dry vegetation). A second step of the analysis conducted at a smaller space scale, from the surrounding ecosystems of the cultivated areas to the inside of these ones, gave the same result. The House Mouse constituted the majority of the captures in the agricultural ecosystems (56% for the total and 84% for sugar cane specifically). This species is well represented inside the cultivated area and poorly outside. The Ship Rat is well represented in the "savannah" and "thorn-scrub", and in tropical rain forest, habitats that surround sugar cane and banana fields respectively. Statistically less numerous than the others, the Norwegian Rat was nevertheless well represented in the cultivated area devoted to watermelon and cassava, and concentrated in the field margins. The build-up and the optimisation of strategies for controlling the alien rodents in tropical islands are discussed in relation to these results. The build-up of sampling strategies to evaluate epidemiological and environmental risks due to these alien rodents is also discussed. This last discussion was done in the light of a new result showing that 57% of sampled Guadeloupe House Mice hosted Leptospira interrogans on their kidneys.