Mount Apo Natural Park (MANP) is an important forest reserve in most part of Region XI and XII because of its watershed importance. However, the MANP may also threatened by habitat modification that may alter most of its water resource. Thus, this study was conducted to assess the abundance of freshwater fish and analyze the physico-chemical properties like water temperature, pH, turbidity, dissolved oxygen (DO), total dissolved solids (TDS), electric conductivity (EC), oxidation-reduction potential (ORP) of the two major rivers of MANP. A total of six freshwater fishes consisting of four native and two introduced species were collected and identified in the two sampling stations. The native Barbodes binotatus (Valenciennes 1842) was found to be the most abundant in all the years the survey was conducted. The data on physico-chemical properties showed fluctuations in all year (2012-13 and 2015). High turbidity rate in Marbel River and high water temperature recorded in upper station of Matingao River could have influenced the collection and abundance of freshwater fishes. Shannon diversity index in Marbel River and Matingao River are very low with values of 0.69 (2012-2013); 0.68 (2015) and 0.70 (2012-2013); 0.70 (2015) for the two rivers, respectively. This could be attributed to anthropogenic activities, characteristics and physico-chemical properties of the river.