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The genus <i>Portulaca</i> L. belongs to the monogeneric family Portulacaceae and consists of about 157 species worldwide. In India, it is represented by 11 taxa; among them, <i>Portulaca badamica</i>, <i>Portulaca lakshminarasimhaniana</i>, <i>Portulaca oleracea</i> var. <i>linearifolia</i>, and <i>Portulaca laljii</i> are endemic. So far, the phylogenetic positions of these species have not yet been analyzed. We have reconstructed the Bayesian and maximum likelihood phylogenies based on a combined chloroplast and nuclear DNA sequence dataset to reveal phylogenetic placements of Indian <i>Portulaca</i>. Phylogenetic analyses indicate that all the sampled Indian <i>Portulaca</i> species (except <i>Portulaca wightiana</i>) are placed in the AL clade, which contains most of the known species of the family Portulacaceae. We used reconstructed phylogeny to study the historical biogeography of Indian endemic species by employing S-DIVA analysis. S-DIVA analysis suggested <i>P. lakshminarasimhaniana</i> has origin in India, it may be the result of in situ speciation in India, and <i>P. badamica</i> was dispersed from Africa to India. We have also discussed the systematic placements of endemic species and their morphological relationships with closely allied species. In addition, this study also provides taxonomic treatment for endemic species.