The taxonomic relationship with Rousettus leschenaultii requires further review. Two geographically isolated subspecies of R. aegyptiacus occur in sub-Saharan Africa (Monadjem et al. 2010). Both subspecies occur in the southern African region: unicolor (Gray, 1870) in Angola and leachii (A. Smith, 1829) in the rest of the region (Monadjem et al. 2010). Additional subspecies: princeps is endemic to Principe Island in the Gulf of Guinea and tomensis is endemic to Sao Tome (Korine 2016).

A recent extensive global phylogeny of Red Foxes that included ~1,000 samples from across the species' range found that Red Foxes originated in the Middle East, then radiated out, and that Red Foxes in North America are genetically distinct and probably merit recognition as a distinct species (Vulpes fulva) (Statham et al. 2014).

All Bottlenose Dolphins around the world were previously recognized as Tursiops truncatus, but currently, the genus is considered to be composed of two species: T. truncatus (Common Bottlenose Dolphin) and T. aduncus (the smaller Indo-Pacific Bottlenose Dolphin) (Wang et al. 1999, 2000a,b). The Common Bottlenose Dolphin has a worldwide distribution in tropical and temperate latitudes but exhibits a strong ability to adapt to local conditions, a complex social structure and strong site fidelity which results in considerable habitat partitioning throughout its range. This, in turn, has created strong population differentiation accompanied, in some cases, by marked morphological differentiation. The taxonomy of Bottlenose Dolphins is confused due to this geographical variation, and it is very possible that additional species will be recognized in the future. Three subspecies are currently recognized by the Society for Marine Mammalogy's Committee on Taxonomy (2017) and a recent re-assessment of Tursiops taxonomy worldwide conducted by the International Whaling Commission confirmed their validity (IWC 2018). These subspecies are the Black Sea Bottlenose Dolphin (T. t. ponticus Barabash-Nikiforov, 1940) which differs morphologically and genetically from other forms including those in the nearby Mediterranean Sea (Barabash-Nikiforov 1960, Geptner et al. 1976, Natoli et al. 2005, Viaud-Martinez et al. 2008). The Lahille Bottlenose Dolphin (T. t. gephyreus) (Lahille, 1908), a larger form in the coastal waters of the western South Atlantic Ocean, is morphologically and genetically different from the offshore population in eastern South America (Costa et al. 2015, 2016; Fruet et al. 2011, 2015). The third subspecies is the nominate subspecies that includes the remaining Common Bottlenose Dolphins worldwide (T. t. truncatus (Montagu, 1821)). In the western North Atlantic, two forms, offshore and coastal, are distinguishable on the basis of morphology and ecological markers (Mead and Potter 1995) and have fixed genetic differences (Le Duc and Curry 1997, Hoelzel et al. 1998, Kingston et al. 2009, Rosel et al. 2009, Van Waerebeek et al. 2017a) and according to the recent IWC review the coastal population should be recognized as at least a different subspecies.

Although several geographic populations have been named as species, morphological and genetic data show there is one world-wide panmictic species (Gibbs and Collette 1967, Scoles and Graves 1993).

Meester et al. (1986) recognised three subspecies, including the nominate subspecies (Taphozous perforatus perforatus) from Egypt (where this species was initially described), T. p. sudani Thomas, 1915 from Sudan, and T. p. haedinus Thomas, 1915 from Kenya. However, it remains uncertain how the geographically isolated southern African population (named T. p. rhodesiae, and described from the Shashi-Limpopo confluence; Harrison 1964) is related to these subspecies (Monadjem et al. 2010). T. p. rhodesiae was originally recognised as a subspecies of T. sudani (T. sudani australis), which was previously identified as a distinct species from T. perforatus (ACR 2015).