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Sporotrichosis is a neglected subcutaneous fungal infection that affects humans and animals worldwide caused by species belonging to the genus Sporothrix. This study aims to examine the range of genetic variations, assess molecular epidemiology significance, and explore potential modes of transmission of the Sporothrix species associated with the current sporotrichosis outbreaks in Espírito Santo, Brazil. In this investigation, 262 samples were evaluated, including 142 from humans and 120 from felines, collected between 2016 and 2021. The isolates were identified based on morphological and molecular characteristics. Sexual idiomorphs were determined by mating-type PCR using primers specific to the MAT1-1 and MAT1-2 loci. Amplified fragment length polymorphism (AFLP) was employed to assess the genetic variability of Sporothrix spp. Finally, antifungal susceptibility testing was performed following the CLSI M38-A2 protocol. Of the 142 human samples, 125 were identified as S. brasiliensis and 17 as S. schenckii s. str. The presence of S. brasiliensis was overwhelming (100%) during outbreaks, highlighting the significant role of domestic cats in the emergence of this species. Heterothallism was the only observed mating strategy. However, the MAT1-2 idiomorph was predominant in cases of cat-transmitted sporotrichosis (χ2 = 202.976; p < 0.0001). Our AFLP results show significant intraspecific variability observed among S. brasiliensis isolates in Espírito Santo. Different genotypes forming subgroups within the same population suggest that these isolates do not originate from a single ancestor, indicating multiple emergences. Furthermore, terbinafine was the antifungal with the best results in vitro. However, in clinical practice, itraconazole remains the primary treatment choice. Sporotrichosis continues to advance in the state; therefore, the health system must outline one-health strategies to contain the disease to prevent future epidemics.