Despite the great interest of earthworms for ecologists and the growing use of molecular data in ecology over the past 20 years, molecular techniques have been only rarely applied to earthworm research. In the family Lumbricidae, problematic taxonomy and the variable level of ploidy within and among species are significant difficulties for research on population genetics. Until 1998, allozymes were the exclusive molecular markers for earthworm population studies but they were found to have substantial limitations. The recent development of more promising markers (e.g. microsatellites) provides exciting prospects for the investigation of recent population genetic events and reproductive strategies of lumbricid species. Recent years have also seen some EST projects undertaken on earthworms which will facilitate the investigation of gene expression through the development of microarrays. In this review, emphasis is on the different molecular techniques currently available for addressing lumbricid ecological issues. Recently-developed methods in population genetics and ecological genomics are also discussed. The rapid progress in DNA sequencing technologies will facilitate both the discovery of new genetic markers and the use of genetic and genomic tools for earthworm ecology.