The development of an assay to quantitate chondroitin AC lyase activity of Cytophaga columnaris isolates is described. Assay conditions were defined by using C. columnaris originally isolated from channel catfish Ictalurus punctatus, coho salmon Oncorhynchus kisutch, goldfish Carassius auratus, and striped bass Morone saxatilis affected with clinical columnaris disease. Supernatant and cellular components of broth cultures exhibited strong activity, and rates of chondroitin sulfate degradation ranged from 20.0 to 81.4 μg/(mL.h) for the cell component and from 35.4 to 83.4 μg/(mL.h) for the supernatant. Degradation rates were calculated by simple linear regression analysis, and most correlations ranged from −0.90 to −1.00. The assay provided results within 2–3 h, and the enzyme is active under a wide range of pH (5–9) and temperature (10–50°C) conditions. The assay can be used as a simple diagnostic aid to differentiate C. columnaris from Cytophaga psychrophila, but more importantly, as a quantitative tool to explore any relationship between specific chondroitin lyase activity and columnaris disease.