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My understanding of read mapping is that your generated reads are aligned to a reference sequence. Is the reference sequence/genome necessarily of the same organism or can the same process be applied to closely related species as well?
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You can map to a related species, but most mapping software is designed for mapping to the same organism. Your mapping proportion will drop, and you'll probably miss out on capturing sequence where there has been a substantial change between the species. I have done mapping for environmental samples where I know the general species, but not the specific strain, of a microorganism.
FWIW, Bowtie2 has a "local align mode" that should work a bit better for mapping to closely related species.
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