Germany has three species of high responsibility for conservation that belong to the closely related genera Spergula and Spergularia. A comprehensive sampling including all three species of responsibility from herbarium material and grown from seeds was used to do Sanger sequencing. Four different markers (ITS, trnKmatK, rpl16, trnL-trnF) were sequenced, phylogenetic and network approaches were used to identify closely lineages of the species of interest, infer monophyly of the species and establish first insights into the diversity of the species. Spergula morisonii is widely distributed in Germany and closely related to S. pentandra. The five samples have several haplo- and ribotypes, without a clear geographic pattern. Spergularia segetalis is one of the first branches of Spergularia and shows a clear isolation-by-distance pattern of diversity. Spergularia echinsoperma belongs to a group of European widespread species, but the included samples all share the same haplo- and ribotype. A population genetic study is needed to get a clear picture of the diversity of S. morisonii and Sp. echinosperma in Germany.