We identify two tissue-specific molecules in the sea urchin embryo by an immunofluorescence technique capable of co-localizing monoclonal antibodies on the same tissue section. The technique uses monovalent Fab-fluorochrome conjugates as secondary reagents to avoid cross-talk of subsequent antibody probes. Using this technique, we show that two cell surface molecules are expressed by different cell populations in the embryo. The technique is generally applicable for antibodies regardless of species or subtype specificity, and uses commercially available reagents. The technique provides sufficient amplification and resolution for analytical work, yet is rapid enough for screening procedures. As a fluorescent counterstain, use of the dye 4-acetamido-4'-isothiocyanatostilbene-2,2'-disulfonic acid (SITS) in the protocol provides a distinct fluorescent background staining of the tissue without interference with the specific antibody staining.