Animals and plants have a complex and effective immune system that protect them from invading microorganisms. The mechanisms of immunity are evolutionarily selected throughout host-pathogen interaction to be tolerant to self-antigens and to recognize nonself molecular patterns. Plants and animals share a germ line encoded diversity of receptors capable of nonself recognition. Somatic rearranging of immunological receptors emerges at early stages of vertebrate evolution, allowing these animals to generate an almost unlimited diversity of receptors. Nevertheless, this recombinational system came with a high price: The potential for self-reactivity. In this chapter we will discuss the differences and the striking similarities of the immune mechanisms across different taxa in the context of evolution and the selective pressures that favoured the development of the adaptive immune system and the lymphoid organs.