[2] The largest distribution is in south-east Europe, Albania, Greece, Bulgaria, Romania, the Balkan countries, Turkey, Cyprus, Iran, Iraq (namely the Tigris–Euphrates river system), Azerbaijan, Israel, Syria.

In Romania, according to studies of Czech ornithologist Robert Ritter von Dombrowski,[3] at the end of the 19th century, the pygmy cormorant was present in large colonies in the Danube Delta, Brăila and Ialomița Pond, on Vederoasa Lake (Constanța County), on certain pools and ponds with reeds and willows in Muntenia.

Populations of pygmy cormorant in Romania have dramatically declined, especially in 1960 when, due to the communist agricultural policies, the Great Brăila Island and important parts of Ialomiţa Pond were drained in order to practice agriculture, so the habitats of a great number of aquatic birds were destroyed.

Threats include the drainage and serious degradation of wetlands and their associated woodland, water pollution, disturbance, and poaching as well as drowning in fishing nets.

In Romania, pond drainage located on the inferior course of the Danube for agricultural purposes, the accidental death of birds captive in improvised fishing nets, nest destruction by professional fishermen in order to protect fish resources decreased of the number of individuals which put the species on the International Union for Conservation of Nature (IUCN) Red List as a vulnerable species.

This species is distinguished from the great cormorant and the common shag by its much smaller size (length 64-78cm), lighter build, and long tail.