The objective was to establish the relationship between cardiac autonomic modulation and physical performance of the functional threshold power (FTP_20.95%W.kg^-1). Twenty-nine male cyclists aged 22±3 years participated. The physical performance of the FTP_20.95%W.kg^-1 was 4.3±0.4. A positive relationship of performance with the parasympathetic index (PNS index) at rest, as well as with parasympathetic reactivity and recovery, R² = 0.80, 0.97, 0.96 respectively, p<0.000, was demonstrated. In conclusion, cyclists with higher physical performance had higher parasympathetic activity at rest. As well as greater parasympathetic reactivity and post-P₂₀ recovery. Both the PNS index and the SNS index are parameters to identify adaptation/maladaptation to training intensity, presence of fatigue, monitor and predict physical performance according to functional power threshold in competitive level cyclists. Additionally, it raises a scenario for identification of genetic predisposition to long-term endurance sports.