Validation of houskeeping genes in a mixture of cDNAs of two species
Two possibilities:


Design primers based on differences in the sequences of the gene for the same protein between the two organisms. (Suggested by @Artem)
Identify an aspect of the metabolism of your parasite that is not present in the host, then use enzymes from that pathway. If the parasite is a worm and the host a mammal, for example, you should surely be able to find something.