Identification and quantification of cyanobacteria in water resources is a basic component of cyanotoxin monitoring programmes to effectively allow early alerts of the type of toxins to expect as well as of bloom development. Decisions on the type of analyses required should be made prior to sample collection. On-site analyses are generally less accurate and less sensitive compared to laboratory analyses but are, on the other hand, less expensive and faster with respect to time to result. Samples may therefore require immediate evaluation on arrival in the laboratory to determine if pretreatment is needed prior to appropriate sample storage. For establishing cyanobacterial identification in a laboratory, consultation with experts on cyanobacterial identification is helpful. As cyanobacterial biomass and community composition is highly inconstant in space and time, a quantification approach that is able to follow this variability is valuable. Microscopic counting of cyanobacterial cells, filaments or colonies has the advantage of directly assessing the abundance of potentially toxic taxa.