The choice of the scientific method to be used depends on the question to be investigated, the type of study being performed, and the maturity of the particular subdiscipline. I review the scientific methods frequently used in biology since Darwin, the aspects of the nature of science relevant for teaching and learning about evolution, and some recent studies that tested the theory of evolution and some of its features. I also present some guidelines for teachers, within an inquiry-based instructional framework, to facilitate students' understanding that hypothesis-driven and observation-driven studies are equally important and responsible for the advancement of scientific knowledge in the field of biology, both in the past and in the present.