Short peptide ligands were synthesized to selectively capture spores using microcantilever arrays. Our initial studies focused on the capture of Bacillus subtilis (a stimulant of Bacillus anthracis) spores in liquids. A peptide-ligand-functionalized microcantilever array was mounted on a flow cell filled with a B. subtilis suspension while cantilever deflection was monitored. Also, fifth mode resonant frequency measurements were performed before and after dipping a peptide-ligand-functionalized microcantilever array in a static B. subtilis solution. Both techniques showed selective binding to functionalized cantilevers when compared to arrays functionalized with a similar control (non-binding) peptide. Conclusive confirmation of selective binding was obtained by subsequent examination of the microcantilever arrays under a dark field microscope. The concentration sensitivity, shelf-life of the binding ligands, and their binding efficiency were studied as well.