Technical Abstract: The phylogenetic utility of sequence variation from five chloroplast DNA intergenic spacer (IGS) regions: trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM was examined in the genus Juglans. A total of seventeen taxa representing the four sections within Juglans and an outgroup taxon, Pterocarya stenoptera, were included in the phylogenetic analyses using the maximum parsimony, maximum likelihood, and minimum evolution methods. The cladograms from all the three analyses were concordent with each other and contained three well-supported monophyletic clades corresponding to the three major sections Juglans, Cardiocaryon, and Rhysocaryon. The cladogenesis within Juglans seems to deviate from the evolutionary hypothesis based on the fossil history and biogeographic evidence. The results suggest that: (1) the cpDNA IGS sequence divergence levels observed within and between different sections of Juglans are low; (2) basal placement of the section Juglans in all the three analyses suggests its ancient origin in contrast to fossil evidence, which suggests the earliest divergence of sections Rhysocaryon and Cardiocaryon; (3) the Asian sections, Juglans and Cardiocaryon, have evolved at different rates as compared to Rhysocaryon; and finally (4) the extant taxa may not represent the entire evolutionary history of the genus.