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Andryala(Asteraceae: Cichorieae) is a little‐known Mediterranean‐Macaronesian genus whose taxonomy is much in need of revision. In order to elucidate species relationships in the genus, we performed phylogenetic analyses of nucleotide sequences of the internal transcribed spacers (ITS) and the external transcribed spacer (ETS) of nuclear ribosomal DNA (nrDNA), two chloroplast (cpDNA) markers (trnT‐trnLand trnV‐ndhCintergenic spacers), and one single‐copy nuclear gene (sqs) using Bayesian and maximum parsimony methods of inference. While cpDNA analysis confirmed a previously inferred chloroplast capture event with the sister genus Pilosella, all nuclear markers supported the monophyletic origin of Andryala. However, determining accurate phylogenetic relationships within the genus was quite challenging due to very low levels of nucleotide divergence of all nrDNA and cpDNA markers and a high degree of homoplasy and incomplete lineage sorting in the variable sqsmarker. Although none of the phylogenies were well resolved, all markers identified two well‐supported basal lineages corresponding to the relict species A. agardhii(Spain, Morocco) and A. laevitomentosa (Romania). The remaining Andryala taxa under study, whose relationships were largely unresolved, formed a well‐supported clade (“Major Radiation Group”). The capacity of the markers to resolve taxonomic entities within this group varied. While congruent genetic evidence was found for some taxa, several morphologically unambiguous species could not be distinguished at all with most or even all markers. The extremely low level of genetic divergence among most of the species, in spite of high morphological diversity, along with a basal polytomy found with all markers, suggests their relatively recent and rapid speciation. Phylogenetic analyses of the single‐copy marker advocate for a single colonization event of the common ancestor of two endemic species (A. glandulosa, A. crithmifolia) from the Mediterranean region to Madeira and that of two other endemics (A. perezii, A. pinnatifida) to the Canary Islands. The frequently observed evolutionary pattern of continental dispersion followed by insular speciation also holds for Andryala.