To provide insights into the molecular mechanisms underlying diabetes mellitus, we performed a proteomic study on two diabetic animal models, streptozotocin (STZ)-induced diabetic rats (T1DM) and genetically diabetic (C57BL/6J ob/ob) mice (T2DM). To better understand the recovery process of those diabetic rodents, we examined the effect of hypoglycemic dipeptide Cyclo (His-Pro) (CHP) treatment on the differential expression of pancreatic proteins in both animal models. Oral administration of CHP had an excellent hypoglycemic effect in both animal models, lowering the average plasma glucose level by over 50%. Pancreatic proteins were separated by two-dimensional gel electrophoresis (2-DE) and identified by MALDI-TOF mass spectrometry. This study allowed, for the first time, the identification of 34 proteins that are related to diabetes and potential targets of CHP, a potent anti-diabetic agent for both T1DM and T2DM. The alterations in the expression of these proteins could indicate a tendency for diabetic animals to overcome their diabetic state. These proteins are involved in cellular functions such as metabolism, cellular structure, oxidative stress, as well as signal and energy transduction. Some have already been linked to diabetes, suggesting that the newly identified proteins might also be significant in the etiology of this pathology and should be further investigated. Furthermore, CHP has emerged as a potent tool for both the treatment and study of the molecular mechanisms underlying diabetes. Thus, the findings presented here provide new insights into the study and potential treatment of this pathology.