As part of projects aimed at studying 1) the role of invasive black rat populations in the emergence of zoonotic diseases in Southeastern Senegal, and 2), the evolutionary consequences of parasites in R. rattus and M. musculus invasions in Senegal, we conducted a series of field campaigns throughout the southern part of the country, between May 2012 and September 2015. The objective was to catch commensal (= indoor) small mammals using standard trapping procedures, identify them using morphological or, if needed, molecular tools, and take a number of samples from them upon autopsy, to look for zoonotic parasites and pathogens. Along with data on individual specimens, information on microhabitat were gathered at each trap position. This resulted in the constitution of a dataset of more than 13.000 trapnights, which allowed the capture of 3166 small mammals, all characterized by a series of associated biological, geographical and environmental data. The small mammals concerned are mainly rodents (10 species), and a few species of shrews and hedgehogs. The two invasive rodent species (the domestic mouse Mus musculus domesticus and the black rat Rattus rattus) were the most numerous, exceeding in numbers all the other species pooled. This dataset makes it possible to study coarse to fine-scaled distribution of species of this small mammal commensal community in the southern part of Senegal, as well as the possible determinants of this distribution in terms of habitat preferences and / or interspecific interactions. Combined with data obtained through the treatment of associated biological samples (population genetics, parasite loads, pathogen prevalence…) they make it possible to precise the epidemiological context surrounding zoonotic diseases in which these small mammal species act as reservoirs or vectors.