Determining which underlying traits contribute to differences in whole-animal performance can be difficult when many traits differ between individuals with high and low capacities. We have previously found that migratory (anadromous marine) and non-migratory (stream-resident) threespine stickleback (Gasterosteus aculeatus) populations have genetically based differences in prolonged swimming performance (U(crit)) that are associated with divergence of a number of candidate morphological and physiological traits (pectoral fin size and shape, body shape, pectoral muscle and heart size, and pectoral muscle metabolic enzyme activities). Here, we use F2 hybrid crosses to determine which traits are correlated with U(crit) when expressed in a largely randomized genetic background and a range of trait values for other divergent traits. We found that four of our 12 candidate traits were positively correlated with U(crit) in F2 hybrids and that the combined effects of ventricle mass, pectoral adductor mass and adductor citrate synthase activity accounted for 17.9% of the variation in U(crit). These data provide additional support for a causal role of muscle and heart size in mediating intraspecific differences in U(crit), but indicate that many candidate morphological and biochemical traits do not have a strong effect on U(crit) when disassociated from other divergent traits. However, the limited variation in U(crit) in our F2 hybrid families may have decreased our ability to detect correlations among these candidate traits and U(crit). These data suggest that many traits, interactions among traits and traits not measured in this study affect prolonged swimming performance in threespine stickleback.