Molecular evidence has demonstrated that the traditional concept of this species comprises at least five distinct geographical lineages (Cavraro et al. 2017). One of these has been described as Aphanius almiriensis Kottelat, Barbieri and Stoumboudi 2007.

The Mediterranean killifish is widespread, and remains abundant at many locations within its range. Although its population trend is estimated to be declining or stable, with some subpopulations highly threatened and others having already been extirpated, it is currently assessed as Least Concern.

This species is native to the Mediterranean Sea basin where it is widespread, with 153 confirmed locations as of 2018. It occurs along the coastlines of North Africa, Israel, Lebanon, southern Türkiye, western Greece, the Adriatic Sea basin and western Italy, and island-dwelling subpopulations are found on Corsica, Sardinia, Sicily, Malta and Cyprus. It is absent from Spain (where an introduced subpopulation has reportedly disappeared from the Ebro River delta), the Greek Islands and Aegean Sea basin, with the exception of isolated subpopulations on Euboea (Evia) island and the Ákra Metóchi lagoon in the eastern Peloponnese. Subpopulations formerly inhabiting coastal wetlands in Syria and southern France have been extirpated. It is assumed that the Suez Canal facilitated a recent expansion into the northern Red Sea basin, where it is potentially invasive. However, the invasion of the species to the red Sea has not been confirmed in recent years.

This species' global population trend has not been quantified, but many subpopulations remain locally abundant. Some have already been extirpated, however, and ongoing degradation of coastal wetlands throughout the Mediterranean Basin is estimated to be driving a general decline (see 'Threats'). On the other side, the species also colonised new localities, especially in Italy and might be overall stable.

This species is euryhaline, mostly inhabiting brackish to hypersaline coastal wetlands including lagoons, salt marshes, estuarine channels and artificial canals, many of which retain a connection to the sea. Inland subpopulations are known from a handful of freshwater rivers in Sicily and some oases in North Africa. Many of its habitats undergo significant inter-seasonal or inter-annual fluctuations in abiotic factors such as salinity, temperature and water-level. It displays a preference for densely-vegetated habitats and is a fractional spawner, tending to reproduce between spring and summer, although some subpopulations reproduce once in spring and again in autumn. It exhibits early sexual maturity and rapid growth, both of which are considered adaptations to unstable environments.

Some subpopulations are threatened by pollution from a variety of sources, or drainage of coastal wetlands for agricultural, industrial, touristic or urban development.

This species is not used or traded.

This species is included in Appendices II and III of the Bern Convention and Annex II of the European Union Habitats Directive. Numerous subpopulations occur within the boundaries of protected areas. Most subpopulations are not specifically managed for conservation purposes, but some work has been carried out in Cyprus and Malta.