Labeled antimicrobial peptides and method of using the same to detect a microorganism of interest. In one embodiment, the method involves adding immuno-capture beads to a sample, the immuno-capture beads including capture antibodies coupled to a paramagnetic bead, the capture antibodies being specific for the type of microorganism of interest. After mixing, the target microorganism binds to the capture antibodies. Next, the beads are collected by positioning a magnet close to the sample, and the unbound material is removed from the sample. Then, a solution containing fluorescently-labeled antimicrobial peptide is added to the sample, the labeled peptide binding in great numbers to the immuno-captured microorganism. After removing unbound peptide, the beads are suspended in solution and a magnetic probe is used to collect the beads in a small volume. With the beads thus drawn together, the solution is excited with a laser. Such excitation causes the label to fluoresce, which fluorescence is then detected.