Colour polymorphisms are common in nature, but their evolutionary significance and the mechanisms maintaining them sometimes remain poorly understood. Polymorphic green pythons (Morelia azurea and Morelia viridis) are born either red or yellow. Several processes are proposed to maintain such polymorphisms, and the assumption that colour is adaptive predicts that it may be correlated with a series of life-history and/or ecological traits. We examined 1090 green pythons from northern Australia and New Guinea and reveal strong geographic variation in the frequency of juvenile polymorphism. Some variation is explained by known genetic structure among populations, while stochastic processes (e.g. bottlenecks, founder effects) likely explain remaining variation. The yellow juvenile morph occurs in all populations of M. azurea and M. viridis, whereas the red morph occurs only in some populations of M. azurea and at varying frequencies. Yellow and red juveniles did not differ in morph-specific survival, sex ratios, morphology (tail length, head shape and mass) or diet. We discuss our results in relation to several hypotheses relating to maintenance of colour polymorphisms in nature. Although inconclusive, we are reluctant to suggest that colour is non-adaptive, and encourage additional experimental field research on the significance of polymorphism in these taxa.