Widespread populations of harvester ants Pogonomyrmex have been shown to have an unusual colony genetic structure and genetic caste determination (GCD), hypothesized to arise from hybridization. These populations of P. barbatus and P. rugosus are composed of two distinct, but mutually dependent genetic lineages (referred to as J1 and J2 for P. barbatus and H1 and H2 for P. rugosus). Workers develop from a cross between the two lineages (H1/H2 for example), but their sister queens only develop from within-lineage matings (H1/H1 or H2/H2). Theoretically, genetic caste determination should be costly since many queen-destined eggs are wasted when a colony is not in the reproductive stage. It has been hypothesized that this cost could be outweighed if workers have traits that give colonies a selective advantage in certain environments. Inter-lineage workers do have distinct behavioral traits from putative parental, normal populations of P. rugosus, such as high aggression. To investigate the potential adaptiveness of increased aggression we examined respiration, metabolism and activity level. Specifically, we measured individual worker respiration and overall activity level in flow-through respirometry, comparing inter-lineage workers (both H1/H2 and J1/J2) and workers of non-GCD P. rugosus and P. barbatus. We found that both metabolic rates and overall activity levels were higher for both types of inter-lineage worker (H1/H2 and J1/J2), compared to non-hybrid workers. Inter-lineage workers were much more likely to display continuous respiration, whereas true P. rugosus and P. barbatus were more likely to show discontinuous and slow cyclic respiration. The differences in respiration patterns and activity were consistent across types, suggesting a genetic basis. The higher metabolism and increased aggression behavior do correlate, as has been found across diverse species. However, whether there is a selective advantage for inter-lineage workers is still unclear.