Eisenia fetida and Eisenia andrei are closely related earthworm species that play a crucial part in soil and influence its structure and organic matter cycling. Due to their essential environmental role, they are widely used as model organisms in a vast spectrum of research areas. In this work, we partially sequenced genomes of E. fetida and E. andrei, using Illumina technology (Nano 2 × 250 v2 - MiSeq) and de novo assembly strategy. A total of 3785 and 4258 microsatellite or Simple Sequence Repeat (SSR) markers were identified within E. fetida and E. andrei genomic DNA, respectively. The microsatellite markers will facilitate the analyses of genetic diversity and population genetics studies for the two selected earthworm species and their interspecific hybrids.