This research aims to: (1) find out the significance of managerial ability differences of the civil servant headmaster in SMP Muhammadiyah Kasihan and affiliate headmaster in SMP Muhammadiyah Pundong, (2) find out the differentiating factors of managerial ability of the headmasters in SMP Muhammadiyah Kasihan and SMP Muhammadiyah Pundong. The research type used was field research using qualitative approach with descriptive method conducted in in SMP Muhammadiyah Kasihan and SMP Muhammadiyah Pundong Bantul DIY. Data collection techniques used were observation, in-depth interview, and documentation. Based on the research results, it can be concluded that: (1) The managerial ability of affiliate headmaster in the term of planning is more eager to do innovations or variations meaning that the planning is not exactly in accordance with the nomenclature of Ministry of Education. Seen from the term of management, the headmaster's organization is able to involve the whole stake holders needed in every program. Seen from the implementation, the headmaster tries hard to accomplish the tasks/ activities given even though the results are sometimes not as good as expected. Monitoring and evaluation are done openly and transparently so that no suspicion arises related to the activities reports. (2) The managerial ability of civil servant headmaster in the term of planning is less eager to do innovations or variations meaning that the planning tends to be exactly in accordance with the nomenclature of Ministry of Education. Seen from the term of management, the headmaster's organization has not been able to involve the whole stake holders needed in every program. Seen from the implementation, the spirit or ghiroh in accomplishing tasks/ activities has not been at maximum. Monitoring and evaluation are done but they are less transparent meaning that not every school members is well-informed about the school reports. Keywords:Managerial, Civil Servant Headmaster, Affiliate Headmaster