Biology is a branch of natural science, the most dynamic. The phenomenon of life in living things, save a lot of interesting problems learned. Problem-based learning makes students centered in learning. Research has been conducted to compare students' learning outcomes by using two stay two stray model and problem based instruction. The method used in this research is quasi-experimental method (quasi-exprimental research). From the results of research that has been obtained, it can be concluded that the learning type of problem-based instruction, the kosep structure of plants is very effective for students. This model can train students to be independent and can solve biology especially related to the structure of plants, and train students to look at things in an integrated manner. Model of learning problem based instruction, has a better learning outcomes, compared with the model of learning model two stay two stray.