Different high-altitude native communities may show different autonomic cardiovascular adapting strategies. The present study was undertaken to evaluate and compare the cardiovascular autonomic functions of the high altitude healthy natives residing at two different altitudes of Jomsom, Thini (altitude: 2800 m) and Muktinath, Jharkot (altitude: 3400 m) of South Asian Himalayan Country Nepal. The cross-sectional study included 72 subjects [age=34.19±22.06 years] from Jomsom, 67 subjects [age= 37.55±16.37 years] from Jharkot and 150 subjects [age=41.03±17.91 years] as a Control group from local community Banepa [altitude: 1439 m]. After consent was taken from each participant, responses to Deep Breathing (DB), Orthostatic Tolerance, Valsalva maneuver and Isometric Hand Grip Test (HGT) were studied following standard protocol. One-way ANOVA followed by Tukey’s HSD test in SPSS 17 was used to compare pairs of means (mean±SD) between the groups. Age difference within groups was insignificant. High-altitude natives showed higher basal diastolic blood pressure [Jharkot Vs Control; 77.19±6.67 Vs 70.75±6.69 mmHg, p<0.01] and heart rate [Jharkot Vs Control; 82.62±5.24 Vs 71.25± 6.84 bpm, p<0.01] than local lowlanders. Evaluating Cardio-vagal influence by Deep Breathing Test and Valsalval Maneuver, Deep Breathing Difference (DBD) [Jharkot Vs Control; 31.46± 11.07 Vs 17.42± 13.95 bpm, p<0.01], Expiration to Inspiration [Jharkot Vs Thini; 1.54± 0.19 Vs 1.41± 0.17, p<0.05] and Valsalva Ratio [Jharkot Vs Control; 1.85± 0.27 Vs 1.37± 0.20, p<0.01] were found significantly increased in high-altitude natives. Sympathetic stress assessment by HGT showed higher diastolic blood pressure response (ΔDBP) [Jharkot Vs Control; 24.96± 8.79 Vs 15.74± 13.27 mmHg, p<0.01] in high-altitude natives. Finding of the study suggest that although adaptation in high-altitude natives leads to increase sympathetic activity, it enhances cardiovagal tone over resting heart which may increase with increase in the level of altitude.