Objective Structure of myocardial mitochondria between FMMU albino guinea pigs and pigment ones was compared after exposed to hypoxia. Methods FMMU albino guinea pigs and pigment ones were placed in hypoxic chamber at normal pressure for 7 d,14 d,21 d respectively to make hypoxic model. Cardiac muscle was taken out and the structure of myocardial mitochondrial was observed under electron microscope. Results In the same hypoxia the myocardial ultrastructure of FMMU albino guinea pigs and pigment ones changed in varying degrees. In different hypoxic stage the ultrastructure of the same guinea pigs changed in varying degrees, too. Conclusion Change degrees of myocardial ultrastructure of FMMU albino guinea pigs were lighter than that of pigment ones under hypoxic circumstances. It hinted that the anoxia tolerance of FMMU albino guinea pigs was higher than that of pigment ones.