Ptychodus was named by Agassiz (1834) [Sepkoski's age data: K Albi-u K Camp Sepkoski's reference number: 884. This author and date are according to Giusberti et al. 2018, PBDB ref. 76687.]. Its type is Ptychodus schlottheimii.

It was assigned to Cestraciontidae by Leidy (1873); to Myliobatidae by Woodward (1889); to Heterodontiformes by Itoigawa (1977); to Ctenacanthida by Sepkoski (2002); and to Ptychodontidae by Hay (1902), Jordan (1963), Applegate (1970), Uyeno (1972), Herman (1977), Thurmond and Jones (1981), Case et al. (1990), Shimada (1996), Cappetta and Case (1999), Cicimurri (2003), Niedźwiedzki and Kalina (2003), Everhart and Darnell (2004), Shimada (2006), Shimada et al. (2006), Cahuzac et al. (2007), Shimada and Martin (2008), Shimada et al. (2009), Bourdon et al. (2011), Guinot et al. (2013), Cicimurri et al. (2014), Bice and Shimada (2016), Giusberti et al. (2018), Amadori et al. (2019), Amalfitano et al. (2020) and Maisch et al. (2021).