The earthworm fauna of Croatia is very diverse and rich in species, but still insufficiently explored. Studies have shown that the determination of earthworm species (especially juvenile) on the basis of morphological characteristics is very complex and that large number of lineages, i.e. subspecies can be found within the established species. The study was conducted to determine the diversity of species within the genera Aporrectodea and Lumbricus using analysis of mtDNA COI gene sequences. Using morphological analysis of collected specimens from nine localities of continental Croatia (Zagreb, Samoborsko gorje, Sunger, Kalnik, Ivanščica, Lipik, Orahovica, Osijek and Halaševo) 33 Aporrectodea and 26 Lumbricus specimens were chosen for molecular analyses. A total of 18 haplotypes were identified within the Aporrectodea genus and 16 haplotypes within Lumbricus genus, and phylogenetic relationships were constructed with the sequences from the BOLD database (Europe). Molecular phylogenetic analyses showed that there was no A. caliginosa specimens recorded within specimens belonging to A. caliginosa complex, while high genetic divergence within the established species A. rosea, L. terrestris and L. rubellus was revealed which may indicate new lineages or species of earthworms. It was found that some haplotypes of Lumbricus genus from Croatia and Scandinavia overlap, what can be related to migrations after the last ice age. In order to obtain a complete picture of the variety of earthworm fauna in Croatia, it is necessary to conduct research on larger number of samples.