Objective To compare the organ coefficients and expressions of hypoxia-related genes in Bama and Juema pigs. Method Real-time quantitative PCR was used to detect the changes of hypoxia gene expressions in the heart, liver, spleen, lung, and kidney of Juema and Bama miniature pigs. Results The organ coefficients of kidney and spleen of Juema pigs were significantly lower than Bama miniature pigs (P<0.05 for both). The heart and lung coefficients of Juema pigs were significantly higher than that of Bama miniature pigs (P<0.05 for both).The VEGF and HIF-1α expressions in the lung and kidney in Juema pigs were significantly higher than Bama pigs (P<0.05 or P<0.01). Only the EPO expression in in the lung of Juema pigs was significantly higher than that of the Bama miniature pigs (P<0.05). Conclusions These results indicate that the variation in organ coefficients may be resulted from evolutionary factors such as adaptiveness to environmental physical and energy conditions, pathogens, and energy metabolism demands, etc. in combination. Juema miniature pigs showing a significantly higher expression of hypoxia-related genes than that in Bama minipigs indicate that it has a strong plateau adaptability by higher gene expressions.