Microsporidia are obligate intracellular parasites that were thought to be an 
ancient eukaryotic lineage based on molecular phylogenies using ribosomal RNA 
and translation elongation factors. However, this ancient origin of 
microsporidia has been contested recently, as several other molecular 
phylogenies suggest that microsporidia are closely related to fungi. Most of the 
protein trees that place microsporidia with fungi are not well sampled, however, 
and it is impossible to resolve whether microsporidia evolved from a fungus or 
from a protistan relative of fungi. We have sequenced beta-tubulins from 3 
microsporidia, 4 chytrid fungi, and 12 zygomycete fungi, expanding the 
representation of beta-tubulin to include all four fungal divisions and a wide 
diversity of microsporidia. In phylogenetic trees including these new sequences, 
the overall topology of the fungal beta-tubulins generally matched the expected 
relationships among the four fungal divisions, although the zygomycetes were 
polyphyletic in some analyses. The microsporidia consistently fell within this 
fungal diversification, and not as a sister group to fungi. Overall, 
beta-tubulin phylogeny suggests that microsporidia evolved from a fungus 
sometime after the divergence of chytrids. We also found that chytrid alpha- and 
beta-tubulins are much less divergent than are tubulins from other fungi or 
microsporidia. In trees in which the only fungal representatives were the 
chytrids, microsporidia still branched with fungi (i.e., with chytrids), 
suggesting that the affiliation between microsporidian and fungal tubulins is 
not an artifact of long-branch attraction.