New technologies and scientific discoveries are upon modern man, rendering obsolete at a very rapid pace existing technology. In the maelstrom of all these prodigious changes, some groups of people have not felt the impact of modern science on their lives. It is in this line where the ethnoscience of some select indigenous groups in Mindanao were explored, specifically the ethnoscinece among Subanen in Lapuyan Zamboanga del Sur and the Mansaka in Mabini Compostela Valley. Purposive and snowball sampling were used in selecting the participants. Ethnographic techniques were used in this naturalistic and qualitative study. The researcher immersed in each community using questionnaire, interview guide, individual and focus group discussions, observation checklist, field notebook, and other instruments. Results revealed that the Subanen and Mansaka farmers were mostly 61 years old and have low level of educational attainment. Magical, traditional, and factual procedures and techniques figured prominently among the crop farming practices, food gathering and food preparation among Subanen and Mansaka. Their balyan healer used a combination of magical, traditional, and factual techniques in treating diseases. Therefore, these groups of people retained and preserved their unique identity and natural knowledge despite tremendous impact of modern technologies and discoveries in multifarious disciplines.