I think it depends how divergent your species are (seems like not very divergent if there is hybridization). I would switch to more variable ones, not genes, but microsatellites or even RADseq. Nuclear genes can have some mutation steps between closely related taxa, but then you can not exclude incomplete lineage sorting if you find two "parental" alleles in you presumable hybrid population.

Definitely use microsatellites and RADseq as described by Oleksandr. Also, perform a next-generation morphometric analysis, if possible.  Good luck.

 I think that you must to combine to types of population genetics analyses using mitochoncrial markers and in the other hand other different types of nuclear markers (microsatellites, RADseq) to access in the possible existence of hybridization and introgression. Moreover, to combine morphometric analyses with molecular data would be useful  tools to clarify the existence of reticulation complex events

Thank you everybody!