Heritability is usually estimated with individuals of known relatedness generated using a controlled breeding programme or through response to selection. In this paper, we use two single-locus VNTR DNA fingerprint markers in conjunction with a maximum likelihood method to infer relatedness among pairs of individuals in a captive population of Pacific chinook salmon (Oncorhynchus tshawytscha). Patterns of relatedness inferred from the two DNA fingerprint markers were used to estimate heritability for, and genetic correlations among, several economically and ecologically important traits (weight, length, flesh colour and precocious male maturation). Heritabilities ranged from 0.20 for weight, 0.38 for length, 0.67 for precocious male maturation (‘jacking’) to 0.76 for flesh colour, which are in good agreement with estimates for salmonids generated using classical quantitative genetic methods. This molecular marker-based method allows for the estimation of heritability in wild, long-lived species not easily manipulated for study using controlled breeding programmes.