Hoshinoamide C (<b>1</b>), an antiparasitic lipopeptide, was isolated from the marine cyanobacterium <i>Caldora penicillata</i>. Its planar structure was elucidated by spectral analyses, mainly 2D NMR, and the absolute configurations of the α-amino acid moieties were determined by degradation reactions followed by chiral-phase HPLC analyses. To clarify the absolute configuration of an unusual amino acid moiety, we synthesized two possible diastereomers of hoshinoamide C and determined its absolute configuration based on a comparison of their spectroscopic data with those of the natural compound. Hoshinoamide C (<b>1</b>) did not exhibit any cytotoxicity against HeLa or HL60 cells at 10 μM, but inhibited the growth of the parasites responsible for malaria (IC<sub>50</sub> 0.96 μM) and African sleeping sickness (IC<sub>50</sub> 2.9 μM).