Nuclear and nucleomorph 18S ribosomal RNA genes from six cryptomonads were amplified by the polymerase chain reaction and sequenced. Phylogenetic trees were constructed by distance, parsimony, and maximum likelihood methods for all available cryptomonad nuclear and nucleomorph 18S rRNA sequences. Nuclear and nucleomorph trees are largely congruent and clearly disprove the idea of polyphyletic origins for cryptomonad chloroplasts. Both show the leucoplast-containing Chilomonas as the sister to all photosynthetic cryptomonads. Using 11 cryptomonad nucleomorph sequences gives more convincing evidence than before that cryptomonad nucleomorphs originated from a red alga and are not specifically related to Chloraraehnion nucleomorphs. Both trees show as a clade the genera with nucleomorphs embedded in a chloroplast-envelope invagination into the pyrenoid (Storeatula, Rhinomonas, Rhodomonas). This monophyly of embedded nucleomorphs supports the recent creation of the order Pyrenomonadales for such cryptomonads. Cryptomonads ancestrally having free nucleomorphs are much more diverse. Komma and Chroomonas, with the blue accessory pigment phycocyanin, form a clade, as do Guillardia and Cryptomonas ~, both with the red pigment phycoerythrin. The nucleomorph trees strongly show the blue Chroomonas/Komma clade as sister to all red-pigmented genera, but nuclear sequences support this weakly, if at all, being sensitive to taxon sampling. Red and blue cryptomonads probably diverged early by differential pigment loss. Nuclear sequences provide no clear evidence for the nature of the host that engulfed the ancestral symbiont. Our nuclear trees using an extensive selection of outgroups, and recent evidence from chloroplast DNA, are consistent with but do not positively support the view that the closest relatives of Cryptista (i.e. Cryptophyceae plus Goniomonadea) are the Chromobiota (i.e. Haptophyta plus Heterokonta, the latter including heterokont algae--phylum Ochrophyta), and that Cryptista and Chromobiota are appropriately classified as subkingdoms of the kingdom Chromista. Maximum likelihood often groups Goniomonas with Chilomonas, suggesting that Goniomonas may have lost both nucleomorph and plastid and that the cryptist common ancestor was photosynthetic.