MALDI imaging mass-spectrometry (MALDI-MSI) is a highly informative approach combining morphology with molecular data. It is widely applied in neuroscience, plant science, cancer-biology, biomedicine, including clinical, and preclinical studies, but not for investigation of endogenous peptides/proteins or metabolites in marine invertebrates. We examined the informativeness of MALDI-MSI for analysis of distribution of antimicrobial peptides (arenicins) in the polychete Arenicola marina and concluded that it can be successfully used as a primary rough express screening method.