Intergenic region typing by restriction analysis of the ribosomal internal transcribed spacer (ITS) and mini-exon provide diagnostic markers for some Leishmania. Here, we evaluate restriction analysis of these targets for genotyping and phylogenetic analysis within the Leishmania donovani complex (agents of visceral leishmaniasis). Each method was useful for genotyping of both L. donovani complex strains and Old World Leishmania species. The targets produced less robust groups than gp63 intergenic regions, but support the need for re-evaluation of the taxonomy of the L. donovani complex.