Unfortunately rapid and easy tool for Zygomycetes identification is mandatory. I think the best way to identify them is ITS region sequencing which is certain metod. First should be assessment under microscope and comparision of growth on different media.  Nevertheless biochemical idetification such as carbon assimilation profile could be usefull. I recommend interesting publications: "Carbon assimilation profiles as a tool for identification of Zygomycetes" P. Schwarz et all Journal of Clinical Microbiology Vol. 45 no. 5 2007

"Molecular identification of zygomycetes from culture and experimentally infected tissues" Schwarz et all Journal of Clinical Microbiology 44:340-349, 2006

Normally, it is not too complicated to identify at least the genus of Mucor-like fungi based on microscopic analysis. It is sometimes a good idea to go back to older books that provide you with good drawings. The Zycha book on Mucorales is still a good one, available in many libraries, but unfortunately written in German. Of course you need to check afterwards for changes in taxonomy, which is easy. Sequencing helps, but keep in mind that you must check sequences against morpholgy. And please: Don't forget about considering new species. There is much more in nature than in the books.

Good luck - sincerely jw.

Molecular methods are unfortunately not standardized. With a large variety of species, culture methods and microscopic analysis of sporangiophores remain the basis for identification.

I do not know of which materials You isolate Zygomycetes, but I recommend the keys:

 Fassatiova O. : Moulds and filamentous fungi in technical microbiology. Amsterdam ; New York : Elsevier, 1986

G.S. de Hoog, J. Guarro, J. Gené and M.J. Figueras: Atlas of Clinical Fungi. Centraalbureau voor Schimmelcultures, 2009 (now also: Atlas of Clinical Fungi USB version - http://www.cbs.knaw.nl/index.php/other-publications/272-atlas-of-clinical-fungi-usb )

and others concerning phytopathology

Zygomycetes (Phycomycetes) is a class in fungi. These fungi have diverse morphology and mostly identified by morphology. See H.l. Barnett : Illustrated Genera of imperfect fungi - to identify conidial zygomycetes. Joseph C. Gillman- A Manual of SOIL FUNGI- TO IDENTIFY MEMBERS OF MUCORALES.  Search NET for Mucorales, Entomophthorales and Zoopagales. Search images, compare and try to know the genus and search NET for monographic papers.

Depends on what you want; if in the end you want to publish the results, you probably need to seqeunce the isolates anyway.

However, for routine daily practice classical methods (micromorphology, growth behivour) often are enough. But still then sequencing can be necesary.

For sequencing, the ITS region allows accurate discrimination of genera but not always of species (sometimes it does). The interspecies variability sometimes is too low (

Mucorales by Zycha is the best.

In the book: Hoog GS, Guarro J, Gené J And Figueiras MJ. Atlas of Clinical fungi. 2ed. Utrecht , Centraalbureau voor Schimmelcultures, 2000; page 58-124 there was explanatory chapter, key to the genera, and description of the zygomycota.

This is a describtion of what we used to identify zygomycetes from clnical specimens quite suceccfully:

Buitrago MJ, Aguado JM, Ballen A, Bernal-Martinez L, Prieto M, Garcia-Reyne A et al. Efficacy of DNA amplification in tissue biopsy samples to improve the detection of invasive fungal disease. Clinical Microbiology and Infection. 1-6-2013;19:E271-E277

In oder to improve culture-outcomes, you should incubate cultures at 37°C.  PCR techniques should also work with cultures.

Gerald Benny's website that is dedicated to the zygomycetes may also be a useful resource.

http://zygomycetes.org/index.php

in addition you con contact Dr. Andre Luiz Santiago ( ) ho work with Zygomycetes from dry areas of NE Brazil