Background: The mechanism of aerobic improvement after altitude training (AT) has not been resolved yet. Few studies have looked at microcirculation changes after AT in athletes. Materials and Methods: Thirty-three male rowers were recruited and divided into either the AT (n = 18, altitude 2,280 m) or the sea level training (ST group, n = 15, altitude 50 m) for 8 weeks training. Microcirculation function was monitored using a laser Doppler flowmeter. VO 2peak and ergometer 5 km time trial (Er5k) were conducted. Results: Within the AT group there was an 8.8% increment in VO 2peak from pre-to post-training (4,708.9 -455.2 vs. 5,123.3 -391.2 ml/min, p < 0.01), whereas in ST group there was a 3.1% increase of VO 2peak from pre-to posttraining (4,975.4 -501.1 vs. 5,128.0 -499.3 m/min, p = 0.125). Er5k performance in AT group was significantly improved (1,040.3 -26.3 vs. 1,033.2 -27.5 seconds, p = 0.038), whereas in ST group Er5k performance was not improved (1,059.6 -30.9 vs. 1,060.4 -33.2 seconds, p = 0.819). Postocclusive reactive hyperemia reserve and heat reserve in the forearm of AT subjects increased significantly after 8 weeks. Meanwhile, the AT group's resting blood flow and cutaneous vascular conductance (CVC) of the thigh were higher after AT. For the ST group, resting blood flow and CVC in the thigh decreased significantly at third week post-training. There was a low correlation between the change of VO 2peak and blood flow of the thigh (r = 0.45, p = 0.01). Conclusions: Trained rowers benefit more from 8 weeks of AT than from 8 weeks ST in terms of aerobic capacity. We have found that 8 weeks of AT increases thigh blood flow and improves endothelial function.