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Five accessions of Dipcadi erythraeum, a rare and endemic, bulbous medicinal plant of Thar desert in India, were collected from different districts of Rajasthan (India) to study the intra-specific genetic variation existing in their natural populations. To resolve species specific cytogenetical mechanism leading to evolution of D. erythraeum, mitotic and meiotic analyses were carried out. The karyotypes of various accessions of D. erythraeum were precisely resolved into ten distinct homologous pairs, not into groups of chromosomes. A striking feature observed meiotically is that bivalents are the most frequent association, while multivalent associations were completely absent in any of the PMCs presently analyzed. Almost diploid like behavior of chromosomes has been the hallmark of the PMCs investigated presently. Overall cytogenetical mechanism underlying the speciation and evolution indicates the probable amphidiploid origin of D. erythraeum.