In this report, a brief analysis of the composition of the genetic code is undertaken, a new version of the rules related to its degeneracy is formulated, and the interpretation of the significance of triplet differentiation on the third basis is deepened in the aspect of the revealed principle of limiting gene coding. The latter manifests itself in the neighborhood of triplets mainly with identical or similar values of complementarity indices, which are equal to the total number of complementary bonds of the triplet with the tRNA recognizing it. The “compensatory” role of synonymous substitutions is considered in aspect to preserve the principle of gene coding limitations in the event of mutations leading to amino acid substitutions in a protein. Synonymous mutations are the very important factor in the evolution of genes, and without them, the description and understanding of the evolution of genes is not complete, since synonymous mutations far outnumber mutations leading to substitutions. Based on the performed analysis of mRNAs of various proteins, the total length of which exceeds 100.000 codons, a list of dicodons that are rare and not identified in the analyzed sample is provided. They are dominated, on the one hand, by codons of amino acids (serine, leucine and arginine) encoded by 6 codons, and on the other hand, codons with the CpG dinucleotide. The possible role of complementary codons in stabilizing the mRNA structure is discussed and asymmetry indices are proposed to assess the imbalance in their quantitative content in mRNA. The revealed limitations in mRNA encoding are considered as barriers to gene and genome recoding, which is widely used in synthetic biology. To avoid failures in gene recoding, any modification of its structure should not contradict the restrictions established by nature.