In this article I argue that the methodology in the Johannes Kepler´s work is guided by two principles of Pythagorean nature, they are: (i) sameness is made known by sameness, and (ii) harmony arises from establishing a limit to what is unlimited.By way of hypothesis, I present a general outline, which includes those principles, and I indicate how they are present in Kepler's investigations.I examine two particular cases in the light of that schema. ___________________________________________________________________________________________________The importance given to geometry, regular solid fixation, obsession with harmony and the fact to consider that music and astronomy as sister sciences are just some features of the Pythagorean influence protruding on the surface of the work of Johannes Kepler.However, the presence of Pythagoras in the work of this scientist and philosopher of the 17th century can be traced more deeply on the methodological aspects.