Colour polymorphisms have evolutionary significance for the generation and maintenance of species diversity. Demonstrating heritability of polymorphic traits can be challenging for wild populations of long-lived species because accurate information is required on trait expression and familial relationships. The Australian magpie Cracticus tibicen has a continent-wide distribution featuring several distinct plumage morphs, differing primarily in colour of back feathers. Black or white-backed morphs occur in eastern Australia, with intermediate morphs common in a narrow hybrid zone where the two morphs meet. This study investigated heritability of back colour phenotypes in a hybrid zone population (Seymour, Victoria) based on long-term observational data and DNA samples collected over an 18 year period (1993–2010). High extra-pair paternity (~ 36% offspring), necessitated verification of parent–offspring relationships by parentage analysis. A total of 538 birds (221 parents and 317 offspring) from 36 territories were analysed. Back colour was a continuous trait scored on a five-morph scale in the field (0–4). High and consistent estimates of back colour heritability (h2) were obtained via weighted mid-parent regression (h2 = 0.94) and by animal models (h2 = 0.92, C.I. 0.80–0.99). Single-parent heritability estimates indicated neither maternal nor paternal non-genetic effects (e.g., parent body condition) played a large role in determining offspring back colour, and environmental effects of territory group and cohort contributed little to trait heritability. Distinctive back colouration of the Australian magpie behaves as a quantitative trait that is likely polygenic, although mechanisms responsible for maintaining these geographically structured morphs and the hybrid zone where they meet are unknown.