Please see

Mol Ecol Resour. 2012 Nov;12(6):1190-5. doi: 10.1111/1755-0998.12011. Epub 2012 Sep 15.

SPInDel: a multifunctional workbench for species identification using insertion/deletion variants.

Carneiro J, Pereira F, Amorim A.

Nucleic Acids Res. 2010 Dec;38(22):e203. doi: 10.1093/nar/gkq865. Epub 2010 Oct 4.

Identification of species by multiplex analysis of variable-length sequences.

Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A.

Thank you very much, sir.

I think DNA barcode is the best way for cryptic species.

Maybe these will very useful for you.

Small Mammal Investigation in Spotted Fever Focus with

DNA-Barcoding and Taxonomic Implications on Rodents

Species from Hainan of China (2012)

Next-Generation Sequencing for Rodent Barcoding:

Species Identification from Fresh, Degraded and

Environmental Samples (2012)

DNA barcoding of Neotropical bats: species identification

and discovery within Guyana (2007)

The Role of DNA Barcodes in Understanding and

Conservation of Mammal Diversity in Southeast Asia (2010)