Three new species of Ziziphus (Rhamnaceae) from Maharashtra, India, Z. bhandarii, Z. naikii, and Z. bhansalii are described here. These species occur in isolated fragments of the Deccan thorn scrub forest ecoregion on the Deccan plateau. Their placement in Ziziphus is confirmed by molecular analyses combining nrITS and trnL-F spacer regions. Given this phylogeny is the most robust to date of Ziziphus, a previously proposed intrageneric classification was tested, and the classification was not supported suggesting a need for additional investigations in this genus. The new species are most closely related to three Indian species, Z. horrida, Z. xylopyrus, and Z. caracutta, respectively, which are morphologically similar and sympatric, and are distinguishable from known species based on several vegetative and reproductive characteristics presented here. A diagnostic key to the Ziziphus species known to occur in Maharashtra is provided.