This paper presents the traditional ecological knowledge system (TEKS) of the Matigsalug tribe in mitigating the effects of dengue and malaria in the hinterlands of Marilog District, Davao City, Philippines. Dengue fever and malaria are prevalent in the area during the rainy season. The Matigsalug people are otherwise known as “river people” as they have been occupying the banks of the Davao River. Participants in the study were the tribe’s herbalists, healers (Babaylan), elders, and tribal leaders (Datu or male chieftain and Bai or female chieftain). This inquiry finds that the Matigsalug tribe people heavily practice TEKS in managing natural disasters especially the dreadful dengue and malaria fever. The tribal community sees the essential role of ecological balance in reducing the risks and mitigating the effects of proliferation of disease-carrying mosquitoes. They commonly use homemade lemongrass preparations in lotion and smoke forms to deter mosquitoes. They command their children to stop catching and playing with spiders and frogs. They view the role of these organisms very important in keeping the spread of mosquitoes at bay. The tribal people conduct community cleaning of river bank and backyard at regular intervals during the rainy season.