Carrying out a BlastP on ORF and achieving hits but 2 have the exact same score, evalue and query cover?
If I understand it correctly, you have two subject protein sequences that are exactly the same as your query. You say they are different species, so I guess you made sure they are not the same species and different strains, or subspecies.

I would suggest to now query your nucleotide sequence using blastn against both results (since a priori it could be either species, or neither), and focus on the one that gets a higher score using blastn in your phylogenetic analysis. Due to codon degeneracy, it could be that your blastn results differ between the two.