Technical Abstract: Phylogenetic analyses of extant Juglans (Juglandaceae) using five cpDNA intergenic spacer (IGS) sequences (trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM) were performed to elucidate the origin, diversification, historical biogeography, and evolutionary relationships within the genus. Overall, 3848 characters were sampled, yielding 150 (3.8%) variable sites, of which, 45 (1.03%) were potentially parsimony informative. In all, seventeen in-group (Juglans) and two out-group (Carya and Pterocarya) taxa were analyzed using the parsimony and maximum likelihood methods, which produced concordant trees with three well supported clades corresponding to the sections Juglans, Cardiocrayon (butternuts), and Rhysocaryon (black walnuts). Juglans cinerea from the section Trachycaryon was placed within the black walnut clade, probably suggesting historical introgression of black walnut chloroplast during its evolution in North America. Black walnuts were not well resolved perhaps suggestive of their relatively recent origin and diversification or reticulate evolution within the section. Within butternuts, J. hopeiensis is moderately supported as a sister to J. ailantifolia, J. cathayensis, and J. mandshurica, which were well supported as a clade in all three analyses. The Persian walnut, J. regia and its sister taxon, J. sigillata formed a distinct clade sister to both butternuts and black walnuts. The cladogenesis within the genus Juglans appears to deviate from the evolutionary hypothesis based on the fossil history and biogeographic evidence. The results suggest that: (1) the IGS sequence divergence levels observed within and between different sections of Juglans are low; (2) basal placement of the section Juglans in both the analyses suggests its ancient origin in contrast to fossil evidence, which suggests the earliest divergence of sections Rhysocaryon and Cardiocaryon; (3) the Persian walnuts and butternuts have evolved at different rates as compared to black walnuts; and finally (4) the extant taxa may not represent the entire evolutionary history of the genus.