The research with the aim to know the difference of metacognitive and scientific writing skill of students at ecology topic in biology instruction learned by project-based learning (PjBL) and guided discovery learning (GD) models in class X Madrasah Aliyah Swasta (MAS) Al-Wasliyah has been done. This research is quasi experiment designed as nonequivalent pretest-postest control group design. Reseach sample was determined by cluster random sampling. Class XA was taught with a project-based learning model and XB class with guided discovery learning model. The research instrument used questionnaire for metacognitive skill and description test for scientific writing skill. Data analysis was done by using t student test. The research results showed that there was significant difference of metacognitive skills of students who taught by project-based learning and guided discovery models (tcount = 2.05; P = 0.04) and there was also significant difference of scientific writing skill of students who taught by the project-based learning and guided discovery models (tcount = 2.21; P = 0.03). The research result recommends the implementation of project-based learning model at ecology topic in biology learning process in order to improve the metacognitive and scientific writing skills of the Indonesia students.