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Manufacturing environment in tanning industry has been associated with human diseases caused by biological agents. This paper reports the microbiological contamination of the indoor environment at a group of tanneries in Leon, Guanajuato, Mexico. The microorganisms present in the indoor environment of the tannery industry has been quantified and identified. The bacteria and fungi concentration in almost all cases exceeded the acceptable levels as dictated by Swedish standard and the limit values proposed by the American Industrial Hygiene Association. The indoor/outdoor ratio was determined, revealing poor air quality at the studied sites. This study has illustrated the presence of pathogens, hazardous to humans in indoor environments of tanneries. The identified bacteria by sequencing of 16S rDNA gene, belonged to families: Bacillaceae, Corynebacteriaceae, Enterobacteriaceae, Moraxellaceae, Nocardiopsaceae, Pseudomonadaceae, Staphylococcaceae. Some of which can be categorized as pathogens such as Acinetobacter calcoaceticus, Acinetobacter johnsonii, Nocardiopsis dassonvillei, Pantoea agglomerans, Pseudomonas putida and Staphylococcus gallinarum. In addition, Fungi genuses identified by microscopy were Aspergillus and Penicillium. The yeasts presumptively identified by ChromAgar medium were Candida krusei and Candida glabrata. Some of these identified microorganisms have been correlated with adverse human health effects, especially in individuals with immunocompromised system.