Huanglongbing (HLB), or citrus greening, is a devastating disease of citrus that is debilitating the U.S. citrus industry. The infected trees exhibit yellowing leaves, premature defoliation, and ultimately death of the entire plant. In addition to the devastating impact of HLB alone, infected trees become an easy target for other diseases. This further decreases the fruit yield, shortens the tree life, and complicates management practices. Raman spectroscopy is a noninvasive and nondestructive analytical technique that provides insight on the chemical structure of a specimen. In this study, we demonstrate that utilization of a hand‐held Raman spectrometer in combination with chemometric analyses enables detection and identification of the secondary disease such as blight on HLB‐infected orange trees (HLB + BL). We also showed that using this spectroscopic approach, we could detect and identify canker and distinguish this disease from healthy trees, HLB, and HLB + BL with high accuracy.