Ziziphus comprises approximately 170 species native to the tropics and subtropics. Two economically important species, Z. jujuba and Z. mauritiana, are cultivated for their fruit. Given the economic importance of these two species, we undertook a reexamination of the intrageneric phylogenetic relationships to identify their closest relatives and to test two alternative intrageneric classifications. These two classifications were tested by using a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (trnL-F) genes. The Old World and New World species of Ziziphus formed two separate well-supported clades. The Old World species of Ziziphus are more closely related to Paliurus than to the New World species, thereby rendering Ziziphus paraphyletic. Sarcomphalus is placed within the New World Ziziphus clade, which supports the transfer of Sarcomphalus to Ziziphus. The earlier placement of Condaliopsis in Ziziphus was supported for one species previously placed in Condaliopsis, Z. obtusifolia, but was contradicted for the other Condaliopsis-like species, Z. celata. Ziziphus celata is more closely related to Rhamneae than it is to Paliureae.