Cibacron brilliant red 3B-A (CBR) has been introduced to determine chitosan (CS) concentrations in solution, and several studies applied it to measure chitosan content in pharmaceutical formulations. So far, studies have relied on the absorbance band shift to 570 nm to determine the extent of the CBR – CS interaction. In this study, we show that CBR forms micro- to nanometer sized aggregates with CS, depending on their charge ratio and that other photophysical changes in CBR are induced by this interaction. We found that, besides the bathochromic band shift, aggregation induces emission at 600 nm and emission quenching at 360 nm. We compared changes CS induced in absorbance and fluorescence emission of CBR with the CS monomer glucosamine and poly(allylamine) hydrochloride, which both contain amino groups, and found that similar but less intense photophysical changes also occur. Furthermore, CS-induced circular dichroism in CBR suggests a twisted, chiral structure of these aggregates that should match with the previously published in silico simulations of the structure of CS in solution. The low linear charge density of CS and its chiral conformation are considered responsible for the enhanced photophysical response of CBR interacting with the polycation.