During recent years, policy-makers of higher education in Iran have paid special attention to interdisciplinarity and as a result, many different interdisciplinary programs have been established. Assessing these programs could guide one to understand the challenges, preventives, and the points of strength and weakness which might help to make improvements in future programming. M.A. program in Mathematics Education is one of the cited programs which is the result of combining Natural Sciences with Education. The present study is focused on this program and attempts to qualify it through observing different graduated people in the field from universities of Beheshti, Bahonar (Kerman), Radjai, Islamic Azad University (Science and Research Branch, and the Kerman Branch) who had graduated before oct. 2008. The research has been conducted through questionnaire, observation, making notes, and interview which have been analyzed by data coding and classification. Results clear the challenges M.A. program in Mathematics Education encounters which could help policymakers to improve interdisciplines, especially ones which are the result of combining Basic Sciences with Education.