Statistical mechanics for geophysical flows is a very promising field of research which explains the global organization of the turbulent planetary atmospheres and oceans. The theoretical ideas developed from the past decade have led to some interesting applications in the last few years. The explanation of the Jovian atmosphere organization - the structure, the shape, and the stability of its Great Red Spot for instance - is of the more significant ones. The 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. Various perspectives on climate modeling and operational oceanography and meteorology are discussed thoroughly.