The phylogeny of spiderhunters (Nectariniidae: Arachnothera) was reconstructed by comparing mitochondrial and nuclear DNA sequences of all currently recognized species and with broad geographic sampling of two particularly variable species complexes, the Little Spiderhunter (Arachnothera longirostra) and the streaky spiderhunters (A. modesta and A. affinis). It appears to be a relatively old group, whose diversification was not caused by recent sea-level changes. However, the modern, highly sympatric distribution of the large species in the Sunda lowlands was probably a result of dispersal via recent land bridges. Within the highly variable A. longirostra group, there are substantially diverged taxa in the Philippines that should be considered different species. Within the A. affinis—modesta complex, there are three distinct species and a closely related fourth, which describe a clear allopatric distribution: A. affinis in Java, A. modesta in the rest of the Sunda lowlands (except Sabah), A. magna in the Malayan highlands and mainland Southeast Asia, and A. everetti in the Bornean highlands and Sabah. Depending on whether mitochondrial or nuclear genes were compared, monophyly of the genus was disrupted by a single outgroup sunbird (Hypogramma hypogrammicum) or by all outgroup sunbirds included in the study. The discrepancy between nuclear and mitochondrial results is probably a case of deep coalescence and will require additional markers for resolution.