Technical Abstract: The Zygomycota are an ecologically heterogenous assemblage of non-zoosporic fungi that are comprised of two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested they are artificial and the phylum is polyphyletic. This result stems from the observation that two of four orders of Trichomycetes are actually related to the Mesomycetozoa protists that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S, 5.8S and 28S genes. Tree reconstruction by Bayesian analyses suggested the Zygomycota is paraphyletic. Although 12 clades were identified, only some of these correspond to the 9 orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales, and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpellales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogonales, and Mortierellales which appear more related to the Ascomycota+Basidiomycota+Glomeromycota. The final major group, the insect-associated Entomophthorales, appears to be polyphyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota, but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping morphological characters, and ecology, where possible. This is considered a snapshot of our current phylogenetic perspective of the Zygomycota, which is intended to stimulate further investigations of the group.