Microscopic Identification of Fungi (Yeasts, Molds)

If you observe a probable fungus in the culture plate, colony characteristics are first assessed to determine the broad group of the isolate. Once the initial observations are made, the following microscopic criteria are used to make a genus/species identification of the fungal isolate.

  1. If hyphae are observed, determine the structure of the hyphae. Are they:
    1. Septate or aseptate
    2. Branching (if so, at what angles) or not branching?
    3. Pigmented or not pigmented
    4. Even or uneven in width
    5. Composed of arthroconidia or pseudohyphae
    6. Determine the structure and derivation of fruiting bodies
  2. Visualize the type of conidiation:
    1. The size and shape of the spores or conidia
    2. The size, shape, and arrangement of the spores
    3. Look for the presence of special diagnostic structures: pycnidia, cleistothecia, Hulle cells
  3. If only yeast cells are observed:
    1. Note their size, shape, and arrangement.
    2. Look for the presence of or absence of capsules.
    3. Determine the type of bastoconidiation- are daughter cells single or multiple?

Presumptive identification of fungi based on Direct Microscopic Examination of material from Clinical Specimen.

  1. Hyphae are relatively small (3-6 micrometer) and regular in size, dichotomously branching at 45-degree angles with distinct cross-septa: Aspergillus spp
  2. Hyphae irregular in size (6-50 micrometer), ribbonlike, and devoid of septa: Zygomycetes (Phycomycetes); Rhizopus-Mucor-Absidia
  3. Hyphae small (2-3 micrometer) and regular, some branching, with rectangular arthrospores sometimes seen: found only in skin, nail scrapings, and hair: Dermatophyte group (Microsporum spp, Trichophyton spp, Epidermophyton spp)
  4. Hyphae regular in diameter (3-6 micrometer), parallel walls, irregular branching, septate, dark yellow, brown or hyaline: Phaeohyphomyces spp, Hyalohyphomyces spp.
  5. Hyphae, distinct points of constriction simulating link sausages (pseudohyphae), with budding yeast forms (blastospores) often seen: Candida spp
  6. Yeast forms, cells spherical and irregular in size (5-20 micrometer), classically with a thick polysaccharide capsule (not all cells are encapsulated), with one or more buds attached by a narrow constriction: Cryptococcus neoformans, Cryptococcus spp., nonencapsulated.
  7. Small budding yeast, relatively uniform in size (3-5 micrometer), with a single bud attached by a narrow base, extracellular or within macrophages: Histoplasma capsulatum
  8. Yeast forms, large (8-20 micrometer), with cells appearing to have a thick, double-contoured wall, with a single bud attached by a broad base: Blastomyces dermatitidis
  9. Large, irregularly sized (10-50 micrometer), thick-walled spherules, many of which contain small (2-4 micrometer), round endospore: Coccidioides immitis


  1. Ogasawara, Y., Hiruma, M., & Muto, M. (2003). Nihon Ishinkin Gakkai zasshi = Japanese journal of medical mycology, 44(3), 217–220. https://doi.org/10.3314/jjmm.44.217 
  2. Grishkina, T. A., & Samygin, V. M. (2013). Klinicheskaia laboratornaia diagnostika, (4), 43–45. 
  3. Erukhimovitch, V., Pavlov, V., Talyshinsky, M., Souprun, Y., & Huleihel, M. (2005). FTIR microscopy as a method for identification of bacterial and fungal infections. Journal of pharmaceutical and biomedical analysis, 37(5), 1105–1108. https://doi.org/10.1016/j.jpba.2004.08.010

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

11 thoughts on “Microscopic Identification of Fungi (Yeasts, Molds)

  1. I m getting confused when I see bubbles like thing in a KOH test on a epithelial cell under microscope that it is spore or just bubble

    1. Assad,
      If the morphological shape do not match with demartophytes, these can be air bubble or artefacts, very hard to see without seeing the slide. Its very unlikely to be the spore. Think/remember the morphology of demartophytes features while observing the slides.

  2. hello,
    i am a student biochemistry and i am searching for scientific papers on how to identify fungi (without PCR or other expensive equipment). The only practicle info i can find is what you have written above.
    could you help me please?

  3. hello i am pooja
    i am confused to identify my fungal flora isolated from soil. give me some suugestion or protocol to folloe to identify them by lactophenol cotton blue staining.
    several culture i have isolated , give only filamentous structure after staining .

  4. I am a Clinical Microbiologist; and not comfortable on Practical techniques for Identification of moulds (eg Dermatophytes) from Clinical specimens (eg skin scrappings). I wish you supported the write-ups with pictorial demonstration of techniques and morphologies. Dr Kalu

    1. In our laboratory, which has basic facilities for the culture and identification of molds, we perform only KOH mount, culture in SDA, LPCB mount etc to identify the isolates. We do not perform vast array of biochemical tests, like we do in Bacteriology.

  5. sir
    i am jeevak
    i wanted to request you to write a blog on different types of organisms causing infective endocarditis the valves effected by them .its very confusing and given in a very different manner in different books.i wud be obliged if u do so
    thank you

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