Interpopulation crosses between divergent populations of Tigriopus californicus copepods have revealed breakdown in metabolic and life history traits. This breakdown has been attributed to incompatibilities in the electron transport system and in DNA replication or transcription in the mitochondria. These incompatibilities can manifest as fitness loss in offspring, where some hybrids may display variable life history traits and energy production. T. californicus produce a red carotenoid pigment called astaxanthin from precursors obtained exclusively through their diet. Across taxa, the biosynthesis of red carotenoids is hypothesized to be linked to individual quality, possibly through shared metabolic pathways with oxidative phosphorylation. However, whether some T. californicus hybrids suffer a loss in the ability to produce red carotenoids has not been tested. Here, we tested whether astaxanthin production varied in hybrid copepods and among established recombinant inbred lines (RIL’s) from interpopulation crosses. Further, we tested whether astaxanthin production was related to mitochondrial metabolism and offspring development. We found that copepods from some hybrid lines produced less astaxanthin than copepods from corresponding parental lines, while other hybrid lines did not. Astaxanthin production was not significantly associated with offspring development in RIL’s. Interestingly, we found that astaxanthin was negatively related to ATP production, but was significantly positively related to an enzymatic marker of mitochondrial density and oxygen consumption. These results indicate that astaxanthin production may be influenced by mitochondrial density and the rate of oxidation reactions.