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Dengue Hemorrhagic Fever (DHF) is an important health problem concern at Special Region of Yogyakarta (DIY). This disease spread through a mosquito (Diptera: Culicidae) that infected dengue virus. DHF can be controlled by decreasing mosquito breeding sites that play an important role of their life cycle. The aims of this research are to determine the characteristics of mosquito breeding sites and their relationship to the presence of mosquitoes in endemic and non-endemic area in the Special Region of Yogyakarta. The study was conducted in July to November 2017. Samples were obtained from 100 houses located in Sorosutan and Panjatan Village. Data were analyzed descriptively and use Chi-Square statistical test SPSS 22. From this research, can be known that there are 45 positive larvae containers in Sorosutan Village and 14 containers in Panjatan Village. Characteristics of breeding sites namely the place of container and water colour can affect larvae existence, but the container cover not related with it. The community behavior include drained water reservoirs in the last 1 week are related to larvae, but fish does not increase or decrease larvae in Sorosutan or Panjatan Village.