A large diphtheria epidemic in the 1990s in Russia and neighboring countries underlined the importance of permanent surveillance of the circulating and emerging clones of Corynebacterium diphtheriae, and hence there is a need for highly discriminatory, simple and portable typing methods. In the complete genome sequence of C. diphtheriae strain NCTC13129, we previously identified in silico two clustered, regularly interspaced short palindromic repeat (CRISPR) loci, and developed a macroarray-based method to study polymorphism in the larger DRB locus. We named this method spoligotyping (spacer oligonucleotide typing), analogously to a similar method of Mycobacterium tuberculosis genotyping. Here, we included in the analysis novel spacers of the other CRISPR locus in C. diphtheriae (DRA); both loci were simultaneously co-amplified and co-hybridized against the membrane with 27 different immobilized spacer-probes. The use of additional DRA spacers improved strain differentiation and discriminated within large DRB clusters. The 156 Russian strains of the epidemic clone were subdivided into 45 combined spoligotypes compared to 35 DRB-spoligotypes and only two ribotypes ('Sankt-Peterburg' and 'Rossija'). The spoligotyping method allows digital presentation of profiles and therefore it is perfectly suitable for interlaboratory comparison and database management; it may become a powerful tool for epidemiological monitoring and phylogenetic analysis of C. diphtheriae.