Meat yield, expressed as the ratio of somatic tissue weight (flesh or meat weight) to total weight, is extensively used in the Atlantic Canadian mussel culture industry as a measure of product quality and market suitability at harvest. Atlantic Canadian mussel populations typically exhibit high genotypic variability with stocks at most sites consisting of mixtures of Mytilus edulis, M. trossulus, and their hybrids in widely varying proportions. In this paper, we examine relationships among genotypic variability, shell and somatic tissue weight, and their effect on measurement of meat yield. We further compare these relationships in populations grown from indigenous seed collection with those derived from transferred seedstock, and across different year classes within sites. Within 10 of 13 samples, M. edulis were greater than M. trossulus in shell length. Within all samples, weights of somatic tissue (flesh weight) and shell varied significantly with shell length. M. edulis typically had greater flesh and shell weights than M. trossulus. Hybrids tended to have intermediate values. Similar genotype-dependent relationships between shell weight and shell length occurred in all year classes taken from the same site. However, flesh weight relationships with shell length were inconsistent among year classes. Within-sample genotype-dependent relationships between flesh weight and shell length evident in indigenously-reared populations did not always persist in transferred populations. Meat yield was not significantly related to shell length. Meat yield was significantly greater in M. trossulus than in M. edulis in 12 of the 13 samples. Similar within-sample relationships between meat yield and genotype were evident among year classes and between indigenously-reared and transferred populations with M. trossulus having greater meat yields than M. edulis. Averaged over all samples, mean meat yield in M. trossulus was 7.4% greater than in M. edulis. Possible industry implications of these genotype-dependent differences are discussed.