The scrub pythons (Morelia amethistina complex) are revised based on museum specimens and new material recently collected in eastern Indonesia. Morelia kinghorni (formerly M. amethistina kinghorni) and M. amethistina (formerly M. amethistina amethistina) are recognized as species, and three new species are described. The phylogenetic relationships of scrub pythons are resolved using morphological and molecular characters Scrub pythons are most closely related to Morelia boeleni and have undergone both ancient divergences and a relatively recent radiation. The distribution of scrub pythons corresponds well with areas of endemism recognized in earlier studies of other taxa. Their distribution and evolution appears to have been shaped by combined effects of dispersal and vicariance. Scrub python populations exhibit interesting color and pattern polymorphism and ontogenetic change, and these characteristics vary among populations.