Upper Miocene (~6 Ma) sediments from a north-south transect of Ocean Drilling Program Holes 848B, 849B, 850B, 851B across the equator in the Eastern Pacific Ocean record an episode of unusual skeletal variability associated with the silicoflagellate Bachmannocena diodon subsp. nodosa (Bukry) Bukry, 1987. Skeletons in this plexus persisted for between 55,000 and 75,000 years and include an arch across a 2-sided basal ring, a highly unusual morphology for the genus. Groups of skeletal morphotypes were common within the plexus episode, and occur in a systematic sequence that is consistent between sites. As a result of this study, silicoflagellates previously placed in the genus Neonaviculopsis Locker and Martini, 1986 are now considered part of the Bachmannocena diodon subsp. nodosa plexus.