Specimens nominally identified as this species from the Philippines and Indonesia are likely to be incorrect identifications of the similar species Sardinella lemuru (Willette and Santos 2013). Recent analysis of micro-satellite markers suggests genetic differentiation of this species between the Gulf of Oman and the coast of India (Sebastian et al. 2017). Subsequent sub-structuring of this species within India revealed genetic differentiation between samples obtained from Mumbai and Mangalore on the western coast of India and the samples obtained from the southwest and eastern coast of India (Calicut, Kollam, Trivandrum, Chennai and Vizag: Sebastian et al. 2017).

Although it was only recently described (Wada et al. 2003), the separate species identity of Omura's Whale, Balaenoptera omurai, is now well established phylogenetically (Sasaki et al. 2006). It was formerly regarded as a pygmy form of Bryde's Whale (B. brydei/edeni), but it is not closely related to that group, lying outside the clade formed by the Sei Whale (B. borealis) and two forms of Bryde's Whales). The morphology of Omura's Whale is quite distinct from those of Bryde's Whales and other known baleen whales, but its colouration resembles that of the Fin Whale (B. physalus) while lacking lateral rostral ridges (Wada et al. 2003). To date (December 2017), the only genetically confirmed observations of living Omura's Whales are of 18 biopsied individuals in an apparently resident population off northwestern Madagascar (Cerchio et al. 2015). Specimens collected in 1976 in the Solomon Sea (Ohsumi 1978) and in 1978 in the eastern Indian Ocean (Ohsumi 1980) were originally taken under a scientific permit for Bryde's Whales and were subsequently genetically identified as Omura's Whales (Wada et al. 2003). LeDuc and Dizon (2002) genetically analysed specimens of small Bryde's Whales from the Bohol Sea, Philippines, and found that they segregated phylogenetically outside the Sei/Bryde's Whale clade and basal to B. edeni/B. borealis. From a comparison of the published phylogenies, Sasaki et al. (2006) concluded that these specimens corresponded to Omura's Whale. Yamada et al. (2008) identified 24 skulls from a whaling operation in the Philippines as Omura's Whales.

Formerly considered a subspecies of Acomys cahirinus. See Musser and Carleton (2005) for details concerning the relationship between Acomys dimidiatus and A. cahirinus.