Like diatoms and brown algae, they have also fucoxanthin, an oxidized isoprenoid derivative that is likely the most important driver of their brownish-yellow color.

[6] The cells typically have two slightly unequal flagella, both of which are smooth, and a unique organelle called a haptonema, which is superficially similar to a flagellum but differs in the arrangement of microtubules and in its use.

[7][8] The chain length of the chrysolaminarin is reportedly short (polymers of 20–50 glycosides, unlike the 300+ of comparable amylose), and it is located in cytoplasmic membrane-bound vacuoles.

[12] The haptophytes were first placed in the class Chrysophyceae (golden algae), but ultrastructural data have provided evidence to classify them separately.

[13] Both molecular and morphological evidence supports their division into five orders; coccolithophores make up the Isochrysidales and Coccolithales.