Sympatric speciation occurs without strict vicariance and is thought to often be driven by ecological specialization of subpopulations that eventually diverge genetically and phenotypically. Distinct morphologies between sympatric populations occupying different niches have been interpreted as such differentiating adaptive phenotypes, yet differences in performance and thus adaptiveness between them were rarely tested. Here, we investigated if divergent body shapes of two sympatric crater lake cichlid species from Nicaragua, one being a shore-associated (benthic) species while the other prefers the open water zones (limnetic), affect cruising and sprinting swimming abilities - performances particularly relevant to their respective lifestyles. Furthermore, we investigated species differences in oxygen consumption across different swimming speeds and compare gene expression in gills and white muscle at rest and during exercise. We found a superior cruising ability in the limnetic Amphilophus zaliosus compared to the benthic A. astorquii, while sprinting was not different, suggesting that their distinct morphologies affect swimming performance. Increased cruising ability in A. zaliosus was however linked to a higher oxygen demand, during activity (but not rest), indicating different metabolic rates during exercise - a hypothesis supported by coinciding gene expression patterns of gill transcriptomes. We identified differentially expressed genes linked to swimming physiology, regulation of swimming behaviour and oxygen intake. A combination of physiological and morphological differences may thus underlie adaptations to these species’ distinct niches. This complex ecological specialization likely resulted in morphological and physiological trade-offs that contributed to the rapid establishment and maintenance of divergence with gene flow.