A comparative analysis of full-genome sequences of chloroplast DNA (cpDNA) of the original inbred line 3629 and three extranuclear mutants, which were obtained by the method of mutagenesis induced with N-nitroso-N-methylurea (NMU) and characterized by different level of chlorophyll insufficiency (en:chlorina-7-yellow-green leaves; chlorophyll content (a + b)-67.8% with respect to the line 3629, variegated-10-leaves with white zones; chlorophyll content (a + b)-2.9% with respect to the line 3629 and variegated-13-leaves with yellow zones; chlorophyll content (a + b)-6.1% with respect to the line 3629), has been carried out. Single-parent maternal inheritance of chlorophyll defects was confirmed by analysis of progeny obtained from reciprocal crossbreedings between the original line 3629 and mutants. Chlorophyll mutants carried modified cpDNA unique for each mutant. We anticipate that chlorophyll defect of en:chlorina-7 may control the observed non-synonymous mutations (transitions) in the genes rpoB, psaA and psbB, which encode β-subunit of RNA-polymerase, the A1 apoprotein of chlorophyll a of the photosystem I, P700 and 47 kDa protein of the photosystem II respectively. In variegated-10, it may control mutations in the genes rpoA and rpoC2, which encode α and β" subunits of RNA-polymerase and in variegated-13-two mutations in the ycf3 gene that encodes photosystem I assembly factor.