There is a continuing need for bioprobes that are target‐specific and combine speed of delivery with maintenance of normal cell behaviour. Towards this end, we are developing small pro‐fluorescent molecules that provide such specificity through chemical activation by biomolecules. We have generated a set of BODIPY (boron dipyrromethane) fluorophores, including one that is intrinsically non‐fluorescent but on incubation with cells becomes fluorescent at its target site. Addition of these BODIPY probes to plant cells identifies peroxisomes, as verified by co‐localization with an SKL‐FP construct. Interestingly, in mammalian cells, co‐localization with the mammalian peroxisomal marker SelectFXTM was not observed. These data suggest fundamental differences in peroxisome composition, development or function between plant and animal cells.