The fouling green algae Enteromorpha intestinalis is a cosmopolitan benthic species, which causes green tides in many coastal areas and is used as an indicator species for eutrophication in the Baltic Sea area. The life cycle of E. intestinalis alternates between two morphologically identical reproductive stages, a haploid gametophyte phase and a diploid sporophyte phase. However, it also reproduces through asexual propagation. The reproductive cycles of E. intestinalis in the Baltic Sea and elsewhere are largely unknown. Here we report five polymorphic microsatellite markers developed from enriched genomic libraries. The number of alleles per locus ranged from 7 to 25.