The diagnostic morphological characters of the subfamily Oxudercinae (Teleostei, Acanthopterygii, Perciformes, Gobioidei, Gobiidae) (Nelson, 1994), were defined by Hoese (1984).
Murdy (1989) proposed a complete morphology-based cladistic revision of this group. This revision was very welcome to mudskipper taxonomy, which has been intricate and chaotic ever since the 17th century.

Murdy defined two monophyletic tribes within the subfamily: Periophthalmini and Oxudercini.

In particular, Murdy described 13 morphospecies of Periophthalmus; nonetheless, five new species of the genus Periophthalmus were subsequently described (P. magnuspinnatus Lee et al., 1995, P. spilotus Murdy & Takita, 1999; P. walailakae Darumas & Tantichodok, 2002; P. darwini Larson & Takita, 2004; P. takita Jafaar & Larson 2008), while P. novaeguineaensis Eggert was redescribed (Jafaar & Larson 2008), and P. variabilis Eggert restored (Jafaar et al. 2009). Therefore, presently this genus includes 18 valid species, and the tribe Periophthalmini (the "mudskippers") includes 34 morphospecies and 7 genera:

Periophthalmus Bloch & Schneider, 1801 (18)
Periophthalmodon Bleeker, 1874 (3)
Boleophthalmus Valenciennes, 1837* (5)
Scartelaos Swainson, 1839 (4)
Apocryptes Valenciennes, 1837* (1)
Pseudapocryptes Bleeker, 1874 (2)
Zappa Murdy, 1989 (1)

Oxudercini include 6 morphospecies and 3 genera:
Oxuderces Eydoux & Souleyet, 1850 (2)
Apocryptodon Bleeker, 1874 (2)
Parapocryptes (Valenciennes, 1837)* (2)

*In: Cuvier & Valenciennes, 1837
The monophyly of Oxudercinae has been recently questioned by some molecular studies (Thacker, 2003). In particular, it seems that Periophthalmini is a paraphyletic group, related with at least some gobiid members of the subfamily Amblyopinae (Akihito et al., 2000; Wang et al., 2001).

Cladogram of the genera of the subfamily Oxudercinae; the group was divided by Murdy (1989) into two monophyletic tribes: Periophthamini (seven genera, above) and Oxudercini (three genera, below). Modified from Murdy (1989), with permission from the author

Evolutionary history of air-breathing vertebrates.
Relative abundance and diversity of each group is roughly proportional to the band width.
Red bars show the cited groups according to Nelson, 1994.
Redrawn from Graham (1997), with permission from Elsevier

At a higher taxonomic level, oxudercine gobies are included in the order Perciformes (series Percomorpha), fishes that have reached high levels of specialization to aquatic life within the Actinopterygii, the "ray-finned fishes" (Nelson, 1994).

Also for this reason, the most peculiar characteristic of mudskippers is the high degree of specialization to amphibious life relative to all living and extinct aquatic vertebrates (Graham, 1997; Clack, 2002).

The ancestors of all the species of the suborder Gobioidei, probably descendants of a primitive group of percoid perciforms (Winterbottom, 1993), invaded the marine coastal areas at least since the Early Eocene, about 50 millions of years ago (Nolf & Stringer, 2003; Bajpai & Kapur, 2004).

No oxudercine fossils are known at present.
The higher species richness, the higher degree of endemism of the Indo-Malayan associations, and the presence of only one species of oxudercine gobies (Periophthalmus barbarus) along the coasts of Western Africa (Murdy,1989), suggest that the whole group originated in the Eastern Tethys.

In particular, the reconstruction of the palaeocurrents' pattern during all the Eocene and Oligocene periods (53.0-23.5 millions of years ago) suggests that the ancestor of P. barbarus could have reached the African continent and the eastern coasts of North and South America in one or more steps if suitable environments had been available (Stille et al., 1996; Ellison et al., 1999). At present though, no oxudercine is known to exist or have existed in the Americas.

During the Miocene (23.5-5.3 millions of years ago), the distribution of these species was probably restrained within the sub-tropical belt, due to a generalized global cooling. About 15 millions of years ago the "Tethydian gateways" between the Atlantic and the Indian Ocean were completely closed by repeated salinity crises of the newly born Mediterranean Sea, caused by the collision of the African and Eurasian continents. Like all other Atlantic and Indo-Pacific fish species, the West-African ancestor of P. barbarus was probably definitely isolated from Indo-Pacific populations.

Present distribution of oxudercine species and limits of the divisional associations (red lines) based on maximal endemism. Numbers indicate the total number of oxudercine species. Modified from Murdy (1989), with permission from the author.
Green lines indicates the distribution of mangrove forests.
Redrawn from UNEP-WCMC, 2005: Coral Reefs and Mangroves of the World

The present distribution suggests a very close linkage of all oxudercine species to mangrove ecosystems and tropical tidal mudflats.
It is possible that this association established in a relatively early phase of their evolutionary history.
Palaeontological data show that mangrove ecosystems had been widespread in the Tethys Sea since the Paleocene-Eocene (60-35 millions of years ago: Ellison et al., 1999), just when the first gobioid fishes appear in the fossil record (see above).

Distribution of modern and extinct mangrove genera based on the fossil record, superimposed on coeval positions of continental land masses.
Redrawn from Ellison et al., 1999, with permission from the first author and from the editor