The distinction of the annual Sagina apetala and S. micropetala (= S. apetala subsp. erecta, S. filicaulis) is based mainly on the position of sepals in fruit and shape and colour of the sepals, but identification of the two species is difficult. A molecular phylogeny of material identified as S. apetala and S. micropetala as well as other species of the genus using two nuclear and two plastid markers showed that there exist two lineages that are sister to each other and can be unambiguously distinguished molecularly. Although many of the morphological characters used in the literature proved useful in distinguishing these two lineages, sepal indumentum is the most reliable character to discriminate between them in Germany. Whereas S. micropetala usually has glabrous sepals, the sepals of S. apetala usually are glandular-pubescent. The chromosome number of 2n = 12 for S. micropetala, here determined for the first time, is identical to that of S. apetala, supporting the close relationship between the two species. Sagina apetala and S. micropetala are sister to S. maritima, an annual species from European coasts, which may imply a coastal origin of the two species. A brief review of the possible origin of other European ruderals from coastal relatives is provided.