Sequences of the nrDNA internal transcribed spacer (ITS) region were analysed for 116 representative species of 59 genera of Compositae-Anthemideae to ascertain the taxonomic position of Matricaria macrotis, a rare and enigmatic species from the E Aegean. The phylogenetic reconstruction indicates that M. macrotis is nested within the genus Anthemis s.str. next to members of A. sect. Maruta. This result is supported by morphological features. The previous inclusion of this species in the genus Matricaria was mainly based on the absence of receptacular scales (pales), whereas several characters of indumentum, achene morphology and achene anatomy support its transfer to Anthemis. The new combination Anthemis macrotis is validated and a lectotype for the basionym designated.