The purpose of this study was to investigate the effect of endurance training on muscle NHE1 and NBC1 gene expression in rat. Male vistar rats (n=20), 4weeks age and 95.7±10.8g in weight were selected and divided into control and training groups randomly. Endurance training were performed for 7weeks that be started with relatively low speed and duration (20m∕min and 20 min respectively) in the first week and reached to 30m∕min and 35min gradually in the last week. NHE1 and NBC1 gene expression determined by Real time-PCR technique in Soleus as a red (oxidative) and EDL as a white (glycolytic) muscle preparation. The between groups differences in variables were determined by independent t-test through REST software .NHE1 mRNA increased in EDL and Soleus by 74% and 51% in trained group in compare with control respectively (P<0/05). NBC1 mRNA expression was also increased in EDL and Soleus by 62% and 41% in trained group, respectively, but not significant in Soleus (P<0/05). In conclusion, these result showed that endurance training  increased NHE1 and NBC1 mRNA expression in both oxidative and glycolytic fibers , Therefore endurance training may improve the capacity for pHi regulation in muscles by lactate independent pathway and  these  increases depend  on transporter and fiber-type specify that are most important in pH regulation.