The earthworms Eisenia fetida and E. andrei are closely related and can hybridise under laboratory conditions, but it is not known if they hybridise under more natural conditions. The two species are genetically well separated, but within E. fetida there is also a deep split forming two well separated mitochondrial lineages. In the present study, 69 Eisenia worms from 23 outdoor (or indoor) composts or other human affected habitats in Sweden and Norway are analysed, using three molecular markers, Cytochrome C Oxidase subunit I (COI), the large 28S ribosomal subunit (28S), and Histone 3 (H3). We confirmed that E. fetida and E. andrei are separate species and, in most cases, are separated by both mitochondrial and nuclear markers, and that the two lineages of E. fetida indeed comprise a single, panmictic species despite the deep mitochondrial divergence. We did find evidence of historical hybridisation between E. andrei and E. fetida, but only in four of the 69 specimens studied.