Critical thinking is one of the basic skills in the 21st century. Based on the TIMSS study (The Trends in International Mathematics and Science Study) on 2007, found that Indonesian student are not able to show some abstract and complex concepts in biology. The student cannot understand the complexity of life creatures and their relationship with the environment. This quasi-experimental research aims to determine: (1) differences of students’ critical thinking skills between PDEODE learning and conventional learning, (2) differences of students’ critical thinking skills between those at higher and lower academic abilities, and (3) the critical thinking skills of students due to the interaction between learning strategy and academic ability. The research design was a pretest-posttest non-equivalent control design. The sample was 40 students of State Senior High School 1 Makassar and Islamic Senior High School Athirah Makassar. The research has been carried out during semester 1 of academic year 2015-2016. Data were obtained by the pre-test and post-test using essay test. Data were analysed using ANACOVA Test. The data analysis showed that learning strategy, academic ability, as well as interaction between learning strategy and academic ability affect the students’ critical thinking skills significantly. PDEODE learning strategy affects the students' critical thinking skills as much as 71.43% higher than conventional learning. High academic ability affects the students' critical thinking skills as much as 67.03% higher than the low academic ability. It is uncovered too that students with low academic in PDEODE class with high academic students in conventional class increase critical thinking skills in the same level. It means that PDEODE learning strategy could help the low academic student to increase their critical thinking skill. PDEODE learning strategy in high academic ability is best one to increase critical thinking skills.