[5] Between 1982 and 1986, a series of ultrastructure studies by Uwe J. Santore found considerable morphological inconsistencies within Butcher's Chroomonas, leading him to identify the new genus Pyrenomonas in 1984.

[6][7] Two years later, he revived genus Rhodomonas and proposed the existence of a clade largely consisting of "reddish-brown cryptomonads".

[10] In 1989, Hill and Wetherbee argued that Rhodomonas was synonymous with Pyrenomonas, triggering an academic debate regarding whether or not each genus should be treated separately.

[12] The earliest reference to Pyrenomonadaceae in an approximately modern sense was made by Gianfranco Novarino and Ian Lucas in their 1993 classification scheme for the Cryptophyceae.

[14] A more comprehensive phylogenetic study in 2014 largely agreed with and expanded upon earlier findings, presenting a preliminary classification scheme with three unnamed clades.