This study examines the association between aerobic capacity and biomarkers of skeletal- and cardiac muscle damage among amateur triathletes after a full distance Ironman. Men and women (N = 55) were recruited from local sport clubs. One month before an Ironman triathlon, they conducted a 20 m shuttle run test to determine aerobic capacity. Blood samples were taken immediately after finishing the triathlon, and analyzed for cardiac Troponin T (cTnT), Myosin heavy chain-a (MHC-a), N-terminal prohormone of brain natriuretic peptide (NT-proBNP), Creatin Kinas (CK), and Myoglobin. Regression models examining the association between the biomarkers and aerobic capacity expressed in both relative terms (mLO2*kg-1*min-1) and absolute terms (LO2*min-1) controlled for weight were fitted. A total of 39 subjects (26% females) had complete data and were included in the analysis. No association between aerobic capacity and cardiac muscle damage was observed. For myoglobin, adding aerobic capacity (mLO2*kg-1*min-1) increased the adjusted r2 from 0.026 to 0.210 (F: 8.927, p = 0.005) and for CK the adjusted r2 increased from -0.015 to 0.267 (F: 13.778, p = 0.001). In the models where aerobic capacity was entered in absolute terms the adjusted r2 increased from 0.07 to 0.227 (F: 10.386, p = 0.003) for myoglobin and for CK from -0.029 to 0.281 (F: 15.215, p < 0.001). A negative association between aerobic capacity and skeletal muscle damage was seen but despite the well-known cardio-protective health effect of high aerobic fitness, no such association could be observed in this study.