Cubitostrea was named by Sacco (1897) [Sepkoski's age data: T Eo-m-l T Mi-u Sepkoski's reference number: 899]. Its type is Ostrea cubitus.

It was reranked as Ostrea (Cubitostrea) by Sacco (1897); it was reranked as Crassostrea (Cubitostrea) by Glibert and van de Poel (1965).

It was assigned to Ostrea by Sacco (1897); to Crassostrea by Glibert and van de Poel (1965); to Ostreinae by Vokes (1980), Squires and Demetrion (1990), Beu et al. (1990) and Perrilliat (1994); to Pterioida by Sepkoski (2002); to Turkostreini by Griffin et al. (2005); to Crassostreini by Squires (2018); and to Ostreidae by Marwick (1960), Woodring (1982), Squires and Demetrion (1992), Wienrich (1999) and Schnetler et al. (2024).