The membrane proteins in photosynthetic and respiratory systems are detected to show considerable sequence similarities to permeases by FASTA algorithm. In the present article, the phylogenetical relationships among these membrane proteins are further investigated by a new method proposed for measuring the distance between paralogous genes in terms of the difference in selective strength and direction as well as by the current method of maximum likelihood. The phylogenetical trees reconstructed by both methods consistently show that the main membrane proteins in photosynthetic and respiratory systems are within the variation range of permeases. In particular, the proposed method, which has the advantage of evaluating the insertion/deletion as well as the nucleotide bases at commonly occupied sites, indicates the following four evolutionary lineages of membrane protein genes; (i) the membrane-anchor domain chains of succinate:quinone oxidoreductase and membrane-anchor domain chains of quinol:fumarate reductase,  (ii) the cytochrome b’s in bc₁ and b₆f complexes, which are closer to amino acid permeases than the first lineage, (iii) the subunit I of cytochrome c oxidase in a closer relation with sugar transporters, and (iv) the core proteins in photoreaction center, which are closely associated with nitrate and formate-nitrite permeases. These results strongly suggest that the above membrane protein genes for respiration and photosynthesis have derived from ubiquitous permease genes, illustrating an example that autotrophic organisms have evolved from heterotrophic organisms by the duplication of pre-existing genes and by the succeeding nucleotide base substitutions and insertion/deletion in the counterpart of duplicated genes.