Flowers represent a relatively unexplored source of antimicrobial peptides of biotechnological potential. This review focuses on flower-derived defense peptide classes with inhibitory activity towards plant pathogens. Small cationic peptides display diverse activities, including inhibition of digestive enzymes and bacterial and/or fungal inhibition. Considerable research is ongoing in this area, with natural crop plant defense potentially improved through the application of transgenic technologies. In this report, comparisons were made of peptide tertiary structures isolated from diverse flower species. A summary is provided of molecular interactions between flower peptides and pathogens, which include the role of membrane proteins and lipids. Research on these peptides is contributing to our understanding of pathogen resistance mechanisms, which will, given the perspectives for plant genetic modification, contribute long term to plant genetic improvement for increased resistance to diverse pathogens.