Relationships among populations (southeast Atlantic and northern Gulf coast, USA) of a ubiquitous, estuarine, harpacticoid copepod (Microarthridion littorale Poppe) were estimated using sequence data from two loci: one mitochondrial [cytochrome b (Cyt b)] and one nuclear [first internal transcribed spacer of ribosomal DNA (ITS-1)]. Copepods were collected from seven estuaries in 1997/98. Allelic phylogenies based on both genes were generally concordant, and suggested that M. littorale populations are structured over large geographic scales (hundreds of kilometers). Three well-supported groups were found in both gene trees comprising clades of alleles sampled from South Carolina, Florida, and Louisiana. Alleles from the Savannah, Georgia sample formed a monophyletic group using the Cyt b data, but this clade was not distinguishable with comparable ITS-1 data. A single specimen from Louisiana was classified in different clades depending on the locus assayed.