Tribe Anthemideae (Asteraceae) is represented in Australia by only nine indigenous species of Cotula and Leptinella. The generic placement of Cotula alpina (Hook.f.) Hook.f. is considered problematic, because it shares the stoloniferous and scapose habit of Leptinella, but lacks corollas in female florets, a trait traditionally considered defining of Cotula. A previous phylogenetic analysis of Leptinella using ITS and chloroplast data showed that the species nested in that genus, but some uncertainty remained because of incomplete sequence data and missing cytological information, and no taxonomic change was made. Here, we use target-capture data from three different sequencing initiatives to reconstruct a phylogeny of Australian native and introduced Anthemideae to resolve this outstanding question. We confirm previous results with a high degree of support and formally transfer Cotula alpina to the genus Leptinella. A lectotype is selected for the basionym, Ctenosperma alpinum Hook.f.