Molecular phylogeny of 52 species of Pinanga (Palmae) were investigated using the internal transcribed spacer (ITS) sequence data of nuclear ribosomal DNA. Polymorphic sequence data were identified in the ITS region of Pinanga, indicating that concerted evolution is not completely homogenizing ITS repeats in the nuclear genome. The strict consensus of Pinanga used in the study showed that the genus is monophyletic. Pinanga rivularis and P. aristata formed the basal clade; followed by P. albescens, P. brevipes, P. veitchii, P. sessilifolia and P. crassipes as sister taxa; and P. disticha, P. watanaiana, and P. pulchella were sister taxa to the clade containing the sampled species of Pinanga used in the study. In general, two major clades were recognized: first, Pinanga from Wallacea, East Malesia and adjacent region clade and second, Pinanga from West Malesia and adjacent region clade. The clade separation was strongly correspond with geographical distribution and it did not support infrageneric classification based on distichous and sprirally triads flower described by Beccari (1886). Conforming phylogenetic tree generated by ITS sequence data and morphological observations appear that habit, size and form of stem, leaf and inflorescence were not useful characters for infrageneric classification of Pinanga. Examination of phylogenetic relationships using combination of morphological characters including pollen morphology, cytological data, nuclear genome size and DNA sequence data are necessary for providing a more accurate picture of phylogenetic relationships and affords the opportunity to garner insights into evolutionary process of Pinanga.