Halisphingosines A (1) and B (2), modified long-chain sphingoid bases, from the marine sponge Haliclona tubifera collected in Brazil, were characterized after conversion to their N-Boc derivatives. The 2R,3R,6R configuration of halisphingosine A, a compound first reported from Haliclona sp. South Korea, was confirmed using a novel CD approach: deconvolution of exciton coupling from mono- and tri-naphthoyl derivatives obtained by derivatization of the natural product. The sensitive CD deconvolution method, applicable to sub-milligram samples, simultaneously predicted the relative and absolute configuration of three stereocenters in halisphingosine A with precision and accuracy. Halisphingosine B was assigned by correlation to halisphingosine A.