A chemical genetic programming apparatus is provided, which enables programming by the application of a chemical genetic algorithm. A CPU 120 includes a tRNA transcripting unit 1201 performing transcription of tRNA from a second portion of DNA, an amino acid translating unit 1202 translating amino acids based on a third portion of DNA and an aminoacyl-tRNA table, an aminoacyl-tRNA updating unit 1203 updating the aminoacyl-tRNA table by a reaction of amino acids and tRNAs, and a phenotype tree generating unit 1205 for generating a phenotype tree by translation based on the aminoacyl-tRNA table and the first portion of DNA, and performs genetic operations on the DNA.