Disclosed are an apparatus for the identification of a ribonucleic acid, whereby not only the molecular weights of digestion products, from which nothing but the nucleic acid residue composition can be understood, but also nucleic acid residue sequence data is obtained from a product ion mass set and thus the identification reliability for the individual digestion products can be remarkably improved; a method for the identification of a ribonucleic acid; and a program and system for the identification of a ribonucleic acid. The method as described above comprises: searching for nucleic acid sequence database by using a fragment mass set indicating the molecular weights and inner structural data of individual oligonucleotides that are obtained by tandem mass spectrometry on digested oligonucleotides formed by chemically or enzymatically cleaving a ribonucleic acid; scoring candidate sequences; among candidate sequences showing the highest scores, referring those showing scores exceeding the threshold as identified sequences; and using these identified sequences in mapping on nucleic acid sequence database including genomic sequences.