Cryptista is a phylum of alga-like eukaryotes. It is most likely related to Archaeplastida which includes plants and many algae, within the larger group Diaphoretickes.

Other characteristic features of cryptomonad mtDNAs include large syntenic clusters resembling α-proteobacterial operons that encode bacteria-like rRNAs, tRNAs, and ribosomal protein genes. Additionally, they are an evolutionarily significant lineage found in mostly marine, glacial and freshwater environments.

Although it has sometimes placed along with Haptista in the subkingdom Hacrobia, within the kingdom Chromista, most recent studies have found that Hacrobia is not a clade. For example, in 2016, a broad phylogenomic study found that cryptists fall within the group Archaeplastida, while haptophytes are closely related to the SAR supergroup.

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