Provided are an apparatus and a method for coding genetic information. An aligning unit aligns sample genetic information, wild-type probe genetic information, and mutant-type probe genetic information, based on a mutation position. A code storage unit stores first orthogonal codes assigned to each of bases located at left and right base regions based on the mutation position and second orthogonal codes assigned to a base located at the mutation position. A coding unit creates first code strings and second code strings. The first code strings are created by assigning the first orthogonal codes, sequentially from left to right, to the bases that make the aligned genetic information and adding a flag that represents the presence or absence of a corresponding base on the genetic information to the assigned first orthogonal codes, and the second code strings are created by assigning the second orthogonal codes to the base located at the mutation position and adding a flag that represents the type of the sample genetic information to the assigned second orthogonal codes.