The structure of ptilomycalin A (1), a marine alkaloid possessing potent antiviral and antibiotic activites, has been determined on the basis of NMR analyses of its trifluoroacetyl (TFA) derivative (2). It has a unique structure consisting of a polycyclic guanidine and a spermidine group, each of which is linked to a 16-hydroxyhexadecanoic acid moiety. The rotational isomerism of the acylated sperimidine moiety of 2 has been studied by comparing the NMR properties of the synthetic trifluoroacetyl derivatives of spermidine (5), dipropylenetriamine (11), diethylenetriamine (12), and pentylamine (13). From these experiments, a plausible conformation of 2 and ptilomycalin A (1) has been proposed as shown in 2c, in which an anion is trapped between the guanidine and spermidine moieties. The TFA derivative 2 acts as a phase-transfer agent. NMR analysis of the stability of the complexes formed between 2 and several organic carboxylates in CDCl3 solutions has been carried out.