The extent of variation in aggressiveness, growth and pigmentation in culture, phytotoxin production and fatty acid profile were determined in a population of 55 isolates ofCercospora piaropi, a fungus used as a biocontrol agent of the aquatic weed water hyacinth (Eichhornia crassipes). Besides differences in the colour of mycelium and diffusible pigments in culture, isolates ofC. piaropigrown under standard conditions differed significantly in their ability to produce the phytotoxin cercosporin, as well as in aggressiveness and growth rate. A positive correlation existed between the ability of the isolates to produce cercosporin and their aggressiveness, and a negative correlation between growth rate and cercosporin production or growth rate and aggressiveness. Based on thin‐layer chromatographic separation of extracts and comparison with beticolin‐1, used as a standard, there was no evidence of production of beticolins. In discriminant analysis, fatty acid methyl ester (FAME) profiles had low resolution for differentiating populations among isolates of the fungus, and the level of resolution was influenced by the age of the colonies. Diffusible pigments in culture and cercosporin production are useful adjuncts to aggressiveness screening for choosing the most effective isolate ofC. piaropifor biological control.