The fungus Rhizopus oligosporus (R. microsporus var. oligosporus) is traditionally used to make tempe, a fermented food based on soybeans. Interest in the fungus has steadily increased, as it can also ferment other substrates, produce enzymes, and treat waste material. R. oligosporus belongs to the R. microsporus group consisting of morphologically similar taxa, which are associated with food fermentation, pathogenesis, or unwanted metabolite production (rhizonins and rhizoxins). The ornamentation pattern, shape, and size of sporangiospores of 26 R. microsporus group strains and two R. oryzae strains were studied using low-temperature SEM (LT-SEM) and LM. This study has shown that: (1) LT-SEM generates images from well-conserved sporangiophores, sporangia, and spores. (2) Robust spore ornamentation patterns can be linked to all different taxa of the R. microsporus group, some previously incorrectly characterized as smooth. Ornamentation included valleys and ridges running in parallel, granular plateaus, or smooth polar areas. Distribution of ornamentation patterns was related to spore shape, which either was regular, ranging from globose to ellipsoidal, or irregular. Specific differences in spore shape, size, and ornamentation were observed between Rhizopus taxa, and sometimes between strains. (3) R. oligosporus has a defect in the spore formation process, which may be related to the domesticated nature of this taxon. It had a high proportion, 10-31%, of large and irregular spores, and was significantly differentiated from other, natural Rhizopus taxa as evaluated with partial least squares discriminant analysis. It is remarkable that the vehicle of distribution, the sporangiospore, is affected in the strains that are distributed by human activity. This provides information about the specificity and speed of changes that occur in fungal strains because of their use in (food) industry.