from http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=snp you can see that you can query the SNP for a given organism using the [ORGN] entrez field

http://www.ncbi.nlm.nih.gov/snp?db=snp&cmd=search&term=%22Apis+Mellifera%22[ORG]

or use ncbi elinks with the snp_taxonomy relationship.

Same for http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=taxonomy: there is a relation named taxonomysnpexp "Snp records associated with taxonomy record (exploded for higher taxa)"