This study was undertaken given the need to develop mathematics modular instruction that integrates Sama students' culture with Science, Technology, Engineering, and Mathematics (STEM) amidst the COVID-19 pandemic. It sought to find whether students exposed to EthnoSTEM-Based Mathematics Instruction (EMI) have significantly better mathematical thinking than those taught with its conventional counterpart (CMI) during modular distance learning. EMI utilized mathematics learning modules that incorporate seaweed farming and mat weaving of the Sama. True Experiment between two groups employing Pre- and Post-tests was done to determine the effects of EMI on mathematical thinking. It was conducted among Grade 7 Sama students from a High School in Tawi-Tawi Province. A researcher-made Mathematical Thinking Test was validated by experts and pilot-tested for item and reliability analyses. Findings revealed that Sama students exposed to EMI have significantly better mathematical thinking than those taught with the CMI. Discussions, conclusions, and recommendations are provided.