Iphigenia brasiliensis is a bivalve mollusk exploited as a shellfish and subsistence resource on the Brazilian coast, mainly in the north and northeast regions. Genetic (allozyme electrophoresis revealed eight gene loci) and morphological variations (multivariate morphometry of valves used 13 linear measurements of traditional and 19 Fourier coefficients of geometric morphometry) were studied, considering the geographic (445 km of the southwest tropical Atlantic), environmental (mangroves and channels of communication with the sea of three estuaries in the state of Rio de Janeiro), and temporal dimensions (over two years). I. brasiliensis showed high levels of genetic variation (the average number of alleles per locus ranged from 2.8 to 3.4, and the average heterozygosity ranged from 0.441 to 0.675). Bayesian analysis of population partitioning showed that the highest LnP(D) value was achieved for K = 3. These results indicated mixed ancestry, possibly oscillations in the dispersion dynamics among the different sampling groups, and temporal oscillations in the population sizes due to the anthropogenic influence on the studied estuaries. The results of morphological variation, inferred by the PERMANOVA from the Fourier analysis, indicated that a similar influence might occur in valves (also, the discriminant analysis showed that different groups could be consistently identified). In this sense, the studied populations may be organized in a dynamic of metapopulations. Finally, these are the first data on morphological and genetic variation of the species in the latitudinal, environmental, and temporal dimensions studied simultaneously, thus providing relevant information for the exploration, management, and conservation of this commercially important species.