Botulinum neurotoxins are classified into seven types (BoNT/A-G), but multiple subtype and mosaic toxins exist. These subtype/mosaic toxins share high sequence identity and presumably the same receptors/substrates with their parental toxins. Here we report that a mosaic toxin, BoNT/D-C, uses different receptors from its parental toxin BoNT/C. BoNT/D-C, but not BoNT/C, binds directly to the luminal domains of synaptic vesicle proteins synaptotagmin (Syt) I and II, and requires expression of Syt I/II to enter neurons. The Syt II luminal fragment containing the toxin binding site can block BoNT/D-C entry into neurons and reduce its toxicity in vivo in mice. We also found that gangliosides increase binding of BoNT/D-C to Syt I/II and enhance the ability of the Syt II luminal fragment to block BoNT/D-C entry into neurons. These data establish Syt I/II, in conjunction with gangliosides, as the receptors for BoNT/D-C, and indicate that BoNT/D-C is functionally distinct from BoNT/C. We further found that BoNT/D-C recognizes the same binding site on Syt I/II where BoNT/B and G also bind, but utilizes a receptor binding interface distinct from BoNT/B and G. Finally, we also report that human and chimpanzee Syt II cannot bind and function as the receptor for BoNT/B, D-C, and G due to a single residue change from rodent Syt II within the toxin binding site, potentially reducing the potency of these BoNTs in humans and chimpanzees.