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This study aimed to determine the effect of the application of project based learning and problem based learning to the students High Order Thinking Skills in the fifth semester of biology education undergraduate students in FMIPA UNIMED. This study used a quasi experimental method with one dependent variable and a study sample of 3 (three) classes determined by random class. Regular class C got treatment for the application of project-based learning, Extension class A got the treatment of application of problem based learning, Extension class B (control) got direct learning treatment. The research instrument was a list of description questions to test students high order thinking skills. Data analysis techniques used covariate analysis (ANACOVA) at a significant level of a = 0.05 with SPSS 23 for Windows. The results showed that there was a significant effect among project based learning, problem based learning and direct learning to high level thinking skills with a value of F = 24,150, P = 0,000. The results of this study stated that the application of project based learning can improve students high order thinking skills.