The aim of the present study was to examine the effects of endurance training on heart rate (HR) recovery after exercise and cardiac autonomic nervous system (ANS) modulation in female marathon runners by comparing with untrained controls. Six female marathon runners (M group) aged 32-40 years and eight age-matched untrained females (C group) performed a maximum-effort treadmill running exercise. Maximal oxygen uptake (VO_2max) was measured during the exercise with a gas analyzer connected to subjects through a face mask. Heart rate, blood pressure and blood lactate were measured before and after the exercise. Rating of perceived exertion (RPE) to the exercise was obtained immediately after the exercise. Holter ECG was recorded and analyzed with power spectral analysis of heart rate variability (HRV) to investigate the cardiac ANS modulation. The M group had significantly higher VO_2max, faster HR recovery after exercise, higher Mean RR, SDRR, HF power and lower LF/HF ratio at rest compared with the C group. The M group also presented greater percent decrease of blood pressure after exercise, although their blood pressure after exercise was higher than the C group. It is suggested that endurance training induced significant alterations in cardiac ANS modulation at rest and significant acceleration of HR recovery after exercise in female marathon runners. Faster HR recovery after exercise in the female marathon runners should result from their higher levels of HRV, higher aerobic capacity and exaggerated blood pressure response to exercise compared with untrained controls.