Ethnoscience learning instruction (ELI) translates available learning materials and uses indigenous language in delivering instruction offers a contextualized learning experience. This study examines the effects of ethnoscience learning instruction on the motivation and academic performance of Grade 7 students at Lilingayon National High School. Specifically, it aimed to: determine the level of students’ motivation as exposed to ELI and to non-ELI; assess the level of students’ academic performance as exposed to ELI and to non-ELI; determine if there is a significant difference in student’s level of motivation as exposed to ELI and to non-ELI; and ascertain if there is a significant difference in student’s level of academic performance exposed to ethnoscience and non-ethnoscience learning instruction. A quasi-experimental research design was employed in the study. The Student’s Motivation Towards Science Learning (SMTSL) questionnaire and a standardized Summative test of the Department of Education 2022 was used to assess the students’ motivation and academic performance respectively. ANCOVA was used to test significant differences between two groups. Findings of the study revealed that the student’s level of motivation as exposed to ELI and non-ELI as very highly motivated and highly motivated respectively. The level of students’ academic performance as exposed to ELI is outstanding and to non-ELI is satisfactory. A significant difference on the levels of motivation in terms of self-efficacy, active learning strategy, performance goal, achievement goal and learning environment stimulation was noted between the ELI and non-ELI, furthermore, there is a significant difference on the levels of academic performance of ELI and non-ELI showing that ELI instruction is effective in improving motivation and academic performance.