Oenanthe aquatica (Apiaceae) and Lycopus europaeus (Lamiaceae) are two hygrophilous plant species found in remnant wetland habitats in agricultural areas. O. aquatica is declining and protected and L. europaeus more common, while still restricted to remnant wet habitats. To gain insights into their population genetic structure, we developed and characterized 16 (O. aquatica) and 15 (L. europaeus) novel polymorphic microsatellite markers from next-generation sequencing. The number of alleles ranged from 1 to 14 for O. aquatica, and from 1 to 9 for L. europaeus. Expected heterozygosity ranged from 0.156 to 0.903 and from 0.333 to 0.749, with a mean multilocus FIS estimate of 0.043 and 0.092 for O. aquatica and L. europaeus, respectively. Overall, these newly developed microsatellite markers showed high levels of polymorphism that will facilitate fine-scaled population genetic studies.