Recent research findings have shown that cooperative learning improves students' thinking skills as it allows them to communicate actively with each other (Johnson, Johnson and Smith, 2014). Therefore, cooperative learning has been proposed by many educators to be implemented in classrooms to produce lifelong learners and critical thinkers (Lunenburg, 2011). The current study investigates the effect of cooperative learning in Biology classroom, on students' learning and achievement of scientific skills. A convenient sample of 120 students from two grade levels, seven and ten, participated in the study in a private school in Beirut, where biology was taught to each class of the two different grades using two different teaching methods: cooperative learning (experimental group) and individualistic-direct learning (control group). Pre- and post- tests were administrated to both groups of each grade to compare students' achievement particularly in scientific skills items before and after intervention. Results of the study show that cooperative learning has a significant effect on students' achievement in learning and practicing scientific skills in grade ten, however no significant effect was shown in the acquisition of new scientific skills for grade seven students.