I advice you first use a conserved gene like the 16S rRNA to detect all the species in that genus. Then you can use a variable gene like the membrane surface protein (msp-3 gene), omp gene, ASP gene, ITS-2, cytochrome b, etc as suggested by Omer. Here are suggested articles:
Hegarty et al. Parasites & Vectors (2015) 8:320 and Maia et al. Parasites & Vectors (2015) 8:138