Statistical mechanics for geophysical flows is a very promising field of research to explain the global organization of the turbulent planetary atmospheres and oceans. The theoretical ideas developed from ten years have lead to some interesting applications in the last few years. The explanation of the Jovian atmosphere organization, of the structure, the shape, the stability of its Great Red Spot for instance, is one of the more striking one. These lecture notes expose some basic concepts of geophysical fluid dynamics and introduce the statistical mechanics for geophysical flows. Applications to the Jovian planets, Earth oceans and atmosphere are treated in details. Perspective on climate modeling and operatinal oceanography and meteorology are discussed.