A molecular phylogeny including c. 75% of all known species belonging to the closely related genera Anthemis and Cota (Compositae, Anthemideae) and based on nucleotide sequences from two plastid regions (psbA‐trnH and trnC‐petN spacers) and one nuclear marker (ITS) is presented. The molecular analyses were supplemented by a multivariate analysis of 25 micromorphological and anatomical characters. The results show incongruences among plastid and nuclear marker sets, which indicate that hybridisation may have played an important role in the evolution of this morphologically diverse plant group. However, molecular and morphological data both support a sister‐group relationship between four perennial species (A. calcarea, A. fruticulosa, A. marschalliana, A. trotzkiana) and the main clades of Cota and Anthemis. We propose segregation of these from Anthemis as a new genus, Archanthemis. With the exclusion of these four taxa, both the nrDNA and the cpDNA datasets support the monophyly of Anthemis. Further molecular and morphological evidence is provided for the generic independence of the genus Cota. The traditional infrageneric classifications of Anthemis and Cota are not entirely supported by the phylogenetic analyses as a picture of intense reticulate evolution among the different lineages emerges.