The different classes of inheritance pattern of plasma gene and allosomes from Mendelian autosomal inheritance pattern discriminate the genome into a fraction, whose main rule is that the fitness of all genes in a set is maximized in the same way. Each set will be selected, that have the capacity to modify the phenotype of the organism in a way to maximally propagate the gene or multiply the gene. The co-existence of such multiple sets in the same genome creates conflict known as intragenomic conflict. The Cytoplasmic Male Sterility (CMS) which is a common feature encountered in plant species, is due to intragenomic conflict. The relationship between intragenomic conflict and CMS, type of conflict, the molecular mechanism of CMS and altruism is discussed in the present chapter.