By using two polyclonal antisera against WH 7803 strain(Synechococcus sp.) and WH 5701 strain (Synechococcus bacillaris) it is possible to detect and to enumerate cells of the two cyanobacterial serogroups. The immunofluorescence technique was used to study the distribution of the two serogroups in the estuarine, coastal and upwelling waters of the Mediterranean Sea surrounding Messina. In the estuarine waters of the Alcantara River (Ionian Sea), the WH 7803 serogroup was present at a concentration in the order of 102 cells ml-1 and the WH 5701 serogroup at a concentration of 5·5 × 102 cells ml-1. In the coastal waters of Messina, where urban and industrial wastes are usually dumped, the concentration of total phycoerythrin-Synechococcus ranged from 1·3 × 102 to 4·1 × 103 cells ml-1; the WH 7803 serogroup accounted for 50-94% of the total population in Ionian stations, whereas the WH 5701 serogroup ranged from 1·4 × 101 to 6·7 × 102 cells ml-1. In the upwelling area (Straits of Messina) both serogroups were found. Vertical distribution of two Synechococcus strains had an opposite trend and their concentrations were of the order of 101-102 cells ml-1. The use of the Scan laser system allows both autofluorescent and labelled organisms to be distinguished in a preparation for optical microscopy. It also allows false-positive cells to be distinguished.