Previous studies have suggested that the woodpecker genus Picus (Aves: Picidae) may not be monophyletic. In order to evaluate this hypothesis, we analyzed DNA sequences from all but two species of Picus, as well as from representatives of all genera in the tribe Malarpicini, within which Picus is nested. We sequenced seven loci (four autosomal, one Z-linked and two mitochondrial) with different evolutionary dynamics. The species currently placed in Picus fall into two subclades that may not form a monophyletic assemblage. Consequently, we propose to place miniaceus Pennant 1769, flavinucha Gould 1834 and mentalis Temminck 1825 in the genus Chrysophlegma Gould, 1850, while the remaining species are retained in Picus. The inclusion in our study of representatives of all genera included in the tribe Malarpicini, a group of woodpeckers which has proven difficult to resolve in several previous molecular studies, also allowed us to determine the earliest divergences within this clade. The results suggest that the low level of basal resolution in Malarpicini is attributable to multiple cladogenetic events in a short period of time rather than insufficient character sampling. This conclusion is supported by the observation of nucleotide insertion-deletions that support mutually exclusive phylogenetic hypotheses in different gene trees. We attribute this pattern of incongruent indels, together with short internodes in the tree, to incomplete lineage sorting.