This species was not widely recognized until 1966, therefore, in literature that predates this time it is often not clear which species of Kogia is intended. No subspecies of K. sima are currently recognized. However, based on mitochondrial cytochrome b gene sequencing, it has been suggested that K. sima consists of two species: one in the Atlantic and the other in the Indo-Pacific (Chivers et al. 2005). Further evidence is required before this can be shown definitively (McAlpine 2018).

G. garamantis, G. vivax and G. quadrimaculatus were previously assessed as separate species in the 2003 Red List, but are now included within Gerbillus nanus.

The Committee on Taxonomy of the Society for Marine Mammalogy (Committee on Taxonomy 2016) provisionally lists the following subspecies: Balaenoptera musculus musculus (Linnaeus, 1758) - Northern Blue Whale (found in the North Atlantic and the North Pacific); B. m. intermedia (Burmeister, 1871) - Antarctic Blue Whale; B. m. indica (Blyth 1859) - Northern Indian Ocean Blue Whale; B. m. brevicauda (Ichihara, 1966) - Pygmy Blue Whale; and B. m. un-named subspecies - Chilean Blue Whale. The nominate subspecies B. m. musculus refers at least to the North Atlantic Blue Whale which was the basis for the first description of the species by Linnaeus. Animals in the North Pacific are similar in size and morphology to North Atlantic Blue Whales and are also regarded as B. m. musculus, pending a genetic comparison of these populations. The Antarctic form B. m. intermedia is distinguished by its large body size and Antarctic distribution in summer. The Pygmy Blue Whale B. m. brevicauda has a number of morphological characteristics that distinguish it from B. m. intermedia and B. m. musculus. It occurs in the Indian Ocean, excluding the Antarctic, from Africa and Madagascar across to Indonesia and Australia, and in the southwestern Pacific, including Tasmania and New Zealand. Blue Whales in the northern Indian Ocean have been tentatively assigned the name B. m. indica, but a clear distinction between B. m. indica and B. m. brevicauda has not yet been established. Blue Whales in the southeastern Pacific are intermediate in size between B. m. intermedia and B. m. brevicauda (Branch et al. 2007a) and are genetically differentiated from both groups (LeDuc et al. 2017). They are provisionally designated as an unnamed subspecies with the common name Chilean Blue Whales. Chilean Blue Whales are genetically most similar to Blue Whales in the northeast Pacific (LeDuc et al. 2017); investigations into the genetic and morphological distinction between these two groups are ongoing. The respective winter ranges of Blue Whales from the eastern South Pacific (Chilean Blue whales) and from the eastern North Pacific may overlap in the eastern equatorial Pacific but their breeding seasons are probably six months out of phase (LeDuc et al. 2017).

Rice's Whale (Balaenoptera ricei) is a distinct evolutionary lineage closely related to Eden's Whale (Balaenoptera edeni edeni), Bryde's Whale (B. e. brydei) and Sei Whale (Balaenoptera borealis) (Rosel et al. 2021). Previously considered an undescribed subspecies of Balaenoptera edeni and referred to as the Gulf of Mexico Whale or the Gulf of Mexico Bryde's Whale, a recent morphological study of Rice's Whale has revealed diagnostic differences in the shape and size of bones in the skull in comparison to the two subspecies of B. edeni. This morphological evidence reinforced earlier findings of significant genetic divergence and fixed DNA differences found in several mitochondrial DNA genes; together these data supported the description of the new species B. ricei . With elevation of Rice's Whale to species status, there is still uncertainty as to whether Eden's Whale and Bryde's Whale, each of which is clearly distinct, represent subspecies of B. edeni or full species.