This study determined the effects of problem-based learning (PBL) on critical and creative thinking skills of second year high school biology students in the Philippines. A quasi-experimental research design using pretest-posttest was employed. One class was exposed to instruction with PBL while the other class was exposed to conventional instruction (Non-PBL). Students exposed to instruction with PBL had higher posttest mean scores in the Critical Thinking Skills Test and Creative Thinking Skills Test than those who were exposed to instruction without PBL. In addition, critical thinking skill appeared to be a significant positive predictor of creative thinking skill. Hence, it is recommended that teachers use the PBL approach in biology classes to enhance the critical and creative thinking skills of the students.