In vertebrates, facultative parthenogenesis (i.e. asexual reproduction by a sexually reproducing species) has been documented in four diverse taxonomic groups, namely sharks, birds, lizards, and snakes. With a single exception, the mode is terminal fusion automixis, where the second polar body fuses with the nucleus of the gamete, restoring diploidy and triggering cell division. The deviating case involves a report of a captive Burmese python (Python bivittatus), a giant Asiatic species common in zoological gardens and the pet trade. Although terminal fusion automixis produces half‐clones of the mother, under this unique case in P. bivittatus, the foetuses were reported as full clones. This conclusion is an apparent anomaly with respect to the mechanism of facultative parthenogenesis reported in all other snakes. In the present study, using genotyping methods, we analyze facultative parthenogenesis in two other species of pythonids and report results that challenge the abovementioned conclusions regarding clonality. Specifically, we report new findings comparable to those reported in other primitive snakes (namely boids), which support the hypothesis of terminal fusion automixis as the mode of facultative parthenogenesis. Furthermore, in light of our new data, we re‐examine the previous report of facultative parthenogenesis in the Burmese python and suggest an intriguing alternative explanation for the earlier findings. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 461–468.