Despite the well-recognized biological importance of protein phosphorylation, non-conventional forms of phosphorylation on histidine and arginine residues have evaded our attention and scrutiny for a long time. This lack of knowledge stems from the inherent chemical instability of phosphohistidine (pHis) and phosphoarginine (pArg), which makes the analysis of these phosphorylations notoriously challenging. Here we present our recent progress in developing novel tools, focusing on fluorescent sensors, to tackle these historically elusive protein modifications.