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Background: Research on the reproductive physiology of Water and Sika deer, an endemic in Korea, still needs to be completed. This study analyzed the ovarian development and morphological characteristics of wild Water deer and Sika deer. Methods: Water deer and Sika deer ovaries were collected from the Korean Peninsula and Russia–Korean Peninsula border during the estrus and pregnancy seasons, respectively. And, morphological and physiological analysis and immunohistochemistry were conducted to confirm the detection of Ca2+ and assess the morphological changes in the ovaries. Results: The results of morphological analysis of ovaries during pregnancy and estrus, the development of the corpus luteum and follicles of Water deer showed similar patterns to other mammals. In contrast, the corpus luteum of Sika deer differed in tissue morphology and composition from Water deer. Ca2+ related to tissue metabolism was detected in the theca cells zone of Water deer on the estrus and was highly detected in the luteum cells zone during pregnancy. The hormone receptor protein expression patterns were generally higher in the ovaries of Water deer on the estrus and the pregnancy than in Sika deer. The expression of LH receptor was relatively low in the lutein cell zone, unlikely that of Water deer. The expression of VEGF was also different from Water deer, and the response in Sika deer was relatively very low compared to Water deer in expressing all proteins-related development. Conclusions: Therefore, the results of the study were shown that the composition of the corpus luteum of Sika deer is not clear compared to Water deer, and there are many differences in the functional and morphological formation of the corpus luteum.