We have examined the common soil zooflagellate Oikomonas mutabilis KEN
T in the light and electron microscope and sequenced its 18s rRNA gene
. It has tubular mitochondrial cristae and a single anterior tinsel ci
lium clothed in a unilateral row of bipartite (or possibly tripartite)
hairs (retronemes) with single terminal filaments, as well with simpl
e non-tubular hairs; it is therefore clearly a heterokont. It differs
from previously studied colourless chrysomonads in the apparent absenc
e of a vestigial leucoplast with eyespot, in the probably bipartite re
tronemes, in the absence of a vestigial smooth cilium, and in the unil
ateral arrangement of the retronemes. Scales appear to be absent. Phyl
ogenetic analysis of its 18s rRNA sequence, however, clearly shows tha
t it is most closely related to the chrysomonads, but it is not specif
ically related to Paraphysomonas. On most trees it is the sister group
to chrysomonads; though its sequence is, therefore, significantly div
ergent from those of all genuine chrysomonads, with the maximum parsin
omy method it can group weakly with Ochromonas. A possible relationshi
p with Ochromonas is also suggested by the presence of numerous large
cortical vacuoles which fluoresce brightly when exposed to ultraviolet
or blue light. Bright short wavelength light kills the cells in a few
seconds. Oikomonas appears to be a third independent example of plast
id loss and the consequent secondary origin of zooflagellates within t
he Heterokonta: our present analysis suggests that Pseudofungi (oomyce
tes and hyphochytriomycetes) also evolved from ochristan algae, by the
loss of chloroplasts, thus providing evidence for at]east four separa
te losses of chloroplasts within Heterokonta. We create a new order (O
ikomonadales), validate the class Oikomonadea for Oikomonas, and inclu
de it with the classes Chrysomonadea, Eustigmatophycea, and Raphidomon
adea in the superclass Limnistia, for which we present a revised class
ification.