In order to detect low copy number sequences in pea using biotin-labelled probes we optimised some aspects of the in situ hybridization technique. We found protoplast preparations to be superior to standard squashes in terms of their signal: noise ratio. Heat and alkali denaturation of chromosomal DNA were both more effective than acid denaturation. A comparison of antibody-fluorochrome and streptavidin-enzyme conjugates showed the streptavidin-alkaline phosphatase conjugate to be the most sensitive detection system. Using the optimised method, we were able to detect a single site for a 13.5 kb legumin gene clone.