Invasive giant hogweeds are infamous in Europe for causing ecological and economic damage, but genetic resources for their study are limited. We used next-generation sequencing to develop a microsatellite library for Heracleum persicum, a widespread invasive in Nordic countries. In addition, these markers were cross amplified with the closely related Heracleum mantegazzianum, Heracleum sosnowskyi, Heracleum sphondylium, and the putative hybrid H. persicum × H. sphondylium, as well as the more distantly related Anthriscus sylvestris. We designed and validated 164 primer pairs. A cost-effective PCR approach with modified forward primer, reverse primer, and fluorescently labeled universal tail was used to test the functionality of each marker. Twenty-five of thirty markers screened on eight geographically distant samples of H. persicum were polymorphic. The number of alleles was 2–4 whereas the expected and observed heterozygosity varied from 0.06 to 0.84 and 0.0 to 1.0 respectively. The cross-species amplification efficiency was 84–100 %, in which 60–76 % of the cross-species amplified markers were polymorphic for Heracleum taxa including H. persicum × sphondylium. Three out of eight of the cross-amplified markers were polymorphic in Anthriscus sylvestris. Ordination revealed a clear genetic structure of Heracleum taxa. Thus, these markers can serve as important genetic resources for understanding taxonomy, population genetics, and phylogeny of giant hogweeds and their hybrids, which in turn, is expected to contribute to invasive species management.