The agave snout weevil (AGW) or sisal weevil, Scyphophorus acupunctatus Gyllenhal is here reported for the first time in St. Croix, U.S. Virgin Islands (USVI) where it threatens Agave eggersiana Trel., a USVI endemic and endangered century-plant. We provide molecular, morphological, and behavioral characters to successfully distinguish the two known Scyphophorus species at all developmental stages. We identified seven new larval characters on the mandibles and characters relating to the chaetotaxy of the labrum and labio-maxillary complex as well as new, putatively informative characters for weevil systematics: chitinized arm of mentum (postlabial strut or postlabial bracon) and the presence of 4 ventral malar setae, instead of 5. In the pupae, the difference in number and placement of rostral setae were also found to be diagnostic. We analyzed two genes, mtCO1 and EF1a, to confirm the identity of the immatures. Phylogenetic analysis of both genes separately and together suggests a clear pattern of substantial phylogeographic structure with specimens clustering by geographic location and this pattern strongly suggests the presence of cryptic species or allopatrically diverged populations. We provide management recommendations for the protection of Agave eggersiana against the threat posed by ASW. We also report, for the first time, the presence of Sphenophorus cubensis (Buchanan) in St. Croix and Scyphophorus yuccae Horn in Panama on Hesperoyucca whipplei (Torr.) Trel. (Asparagaceae: Agavoideae).