Prokaryotic histone-like proteins (Hlps) are abundant proteins found in 
bacterial and plastid nucleoids. Hlps are also found in the eukaryotic 
dinoflagellates and the apicomplexans, two major lineages of the Alveolata. It 
may be expected that Hlps of both groups were derived from the same ancestral 
Alveolates. However, our phylogenetic analyses suggest different origins for the 
dinoflagellate and the apicomplexan Hlps. The apicomplexan Hlps are affiliated 
with the cyanobacteria and probably originated from Hlps of the plastid genome. 
The dinoflagellate Hlps and the proteobacterial long Hlps form a clade that 
branch off from the node with the proteobacterial short Hlps.