A time series of satellite imagery of AVHRR sea surface temperature (SST) and SeaWiFS chlorophyll concentration (CHL) for Hellenic waters are analyzed for the mapping of anomaly distribution in these environmental parameters. The spatial distributions of these anomalies are compared using a Geographic Information System (GIS) in order to identify and map areas of persistent environmental anomaly. These spatial distributions describe areas, which are characterized by highSST/lowCHL and lowSST/highCHL values. Generally, the first pair of anomalies implies the spatial extent of persistent cyclonic gyres while the second pair implies the extent of persistent anticyclonic gyres and upwelling. Such oceanographic features (gyres and upwelling) are processes, which along with eddies and fronts, consist the main factors of water mass mixing, particularly in the upper layer euphotic zone. A seasonal classification of these anomalies is developed because SST anomaly, in particular, is widely accepted as the proxy factor for a variety of oceanic and atmospheric-meteorological phenomena. In addition, lowSST/highCHL areas indicate offshore feeding grounds for many commercially important species, such as small pelagic fish (sardine and anchovy) and pelagic cephalopods (squids). A preliminary comparison of surveyed catch data to lowSST/highCHL areas shows a remarkable relation between species distributions and environmental anomalies. However, the main purpose of this work is the combined mapping and classification of SST/CHL anomalies in SE Mediterranean waters.