Organisms have been formed in the long-term evolution in which natural selection are constantly working. As an outcome, any trait, behavioral, physiological, or morphological, can evolve to achieve the "optimal" phenotype according to a simple and traditional scenario of evolution. However the environment that has a large impact to the fitness is itself other species, such as pathogens, parasites, who also evolve by natural selection. Hence to understand the evolutionary outcome of this process, we must consider the simultaneous evolution between two or more species that evolve simultaneously. This is called coevolution.

I then introduce two themes of the antagonistic interaction of organisms.

First, I focus on the conflict between nuclear genes and mitochondria genes, and show how the antagonistic interaction between nuclear genes and mitochondria genes leads to the evolution of a linear hierarchical uniparental cytoplasmic inheritance in organisms having many mating types (e.g. plasmodial slime molds). Second, I focus on the inter-specific antagonistic interaction. I discuss the gene-for-gene (GFG) interaction between disease-resistance and pathogen virulence, which is the major coevolutionary theatre between plants and their pathogens. Based on the epidemiological model that takes into account the genotypic diversity of host resistance and pathogen virulence, I examine the optimal disease-control of crop plants under the threat of pathogen infection and the threat of the development of pathogen virulence that restores the pathogenicity to the disease-resistance.