Barriers to gene flow in marine environments vary between species and are highly dependent on dispersal ability and habitat discontinuity. Intertidal sand and mud flats are discontinuous areas, separated by other habitat types along a coastline or by subtidal zones. The São Sebastião Channel in eastern Brazil, which is situated between Rio de Janeiro and São Paulo, harbors two intertidal mud flats where populations of the kinorhynch Echinoderes marthae are found, one on the mainland (Araçá Bay) and one on São Sebastião Island (Ilhabela). Here, we investigated the genetic structure of two E. marthae populations across the São Sebastião Channel, in order to contribute to the ongoing debate on biogeography of meiobenthic animals. Based on 628 bp of the mitochondrial CO1 gene, we find that E. marthae shows low levels of structure in the São Sebastião Channel (FST = 0.165), and find evidence of recent demographic expansion across populations.