Lake Ohrid is a distinctive shelter of large number of freshwater organisms originating from the tertiary period, whose close relatives can be found in fossil forms only. For precisely this reason it bears the name "Museum of living fossils". Its remarkable age, continuing existence, geografic isolation, and the permanency of its living conditions - all of these together enabled most of its inhabitants to continue the process of their further evolution up to this day. This also made it possible for the already existing tertiary living forms in the Lake to further evolve into new taxonomic classes including, subspecies, species, even entire families of newly evolved organisms. Thus, the endemism (presence of distinctive, unique organisms), although less underlined than in Lake Baikal, is the feature of the living world of Lake Ohrid, comprising 88% of endoparasitic Infusoria (tiny parasitic organisms), 44% of rabdocelite, and 71% of trikladite (flat worms), 90% of snails, 66% of small crabs, and 60% of fish.

The so-called intralacustric speciation process, particular for old, deep and large lakes in the world, is on-going in Lake Ohrid and it has encompassed even the fish fauna.

The size of the Lake and the quality of its fish fauna underpin its significance in fishing terms. The quality and economic importance of the fish population of the Lake are of a far more higher level than that of the rest of Balkan's lakes, even higher than the shallow and highly productive lakes of the Aegean region.

The fish population of Lake Ohrid comprises 17 native species belonging to four families: Salmonidae (2 species), Cyprinidae (12 species), Cobitidae ( 2 species) and Anguillidae (1 species). Ten species are commercially important for the fishing industry, priority being given to the two endemic and relic trout species - Ohrid Trout and Belvica, with Europian Eel and Plasica following the first two. Several analysis have been carried out since 1929. They have shown that the trout and eel account for 45.6% of the catches. That is why the Lake is also called "Trout Lake". The same analysis has shown that the catchment in the Lake Ohrid, in terms of area units, is 9 kg/ha for the Macedonian part of the Lake. This is caused by the low levels of nutrients and is another indicator of its oligotrophic character.

Ohrid Trout is well-known worldwide and can weight more than 10 kg. However, in the present conditions in the Lake it reaches the weight of 1 kg in the seventh year of its life. The latter type of trout, Belvica, is smaller than the former. It can reach 30 cm in lenghth and weigh up to one kilogram, but rarely does, since this weight can be reached only in the twelwth year of its life. The fish Plasica is caught during winter period and can reach 5 to 15 cm in lenghth. The famous Ohrid Pearl is produced by using special technology for processing its scales.

Alongside these fish species, there are also chub, carp, skobal, grunec, etc.

Due to the main focus on Ohrid Trout in fishing, the Hydrobiological Institute was founded in the far back past, in the year 1934. Its establishment, along with the instalation of its reproducing units, marked the beginnig of Ohrid Trout artificial spawning process aimed at stocking Lake Ohrid with Ohrid Trout progeny. Ever since this process has been continuously advanced. Up til now, the Lake has been stocked by over 520 million pieces of Ohrid Trout offspring cultivated to various ages and sizes - starting from larvae and up to the age of 18 months. Sexually matured fish caught in the Lake are used in the process of "artificial spawning". First roe and milt are pressed out from the fish. Then, they are mixed in the water environment resulting with in situ insemination of the roe. The inseminated roe is then transported into the reproducing units and further nurtured before being stocked into the Lake. The Lake is also stocked with the spawn of the european eel, a species whose natural production circle has been discontinued.

The fauna in the Lake also includes freshwater shells, crabs, sponges, etc. There are four types of sponges in the Lake, amongst which is the most famous endemic round Ohrid sponge that lives in 40-50 m depth.

The Lake's fauna is dominated by various types of algae and superior water plants. Typical for Lake Ohrid is the underwater plant called "hara", that forms a continual ring on the lake's bottom, at the depth of 6 - 15 m.

There are also endemic species in the plankton population (tiny microscopic organisms floating or drifting in the water) - both in zooplankton (animal component) and in phytoplankton (plant component).