Hot springs are like nature’s spas, which include warm and humid aquatic habitats that serve as a sanctuary for a diverse range of microorganisms, including bacteria, archaea, viruses, and eukaryotes fungi. Among these, fungi are one of the most important microorganisms, carrying out essential functions that often go unnoticed but are crucial in accelerating biological processes. These organisms have adapted to survive under a wide range of thermal conditions. While thermophilic fungi can withstand the scorching heat of deserts and hyper-saline conditions, other variants like mesophilic and psychrophilic fungi prefer more moderate and colder temperatures, respectively. The study employs shotgun metagenomic sequencing to obtain a fine-grained taxonomic classification of lesser-known species and microbial eukaryotes. This study aims to explore the relationship between fungal diversity and temperature in three distinct thermal zones; thermophilic (hot spring), mesophilic (plain field), and psychrophilic (semi-frigid zone) zones. The findings of our study demonstrated that there is a notable and positive association between the diversity of fungi and temperature, suggesting that temperature is a key factor in moulding fungal communities. However, it is important to note that further research is necessary to elucidate the underlying causal mechanisms of this relationship. Overall, our study adds to the knowledge of how environmental factors influence microbial diversity and can aid in the development of strategies for the conservation and management of fungal communities. Fungi are essential for many industrial applications, and their role in causing illnesses is also significant, making this research valuable for both scientific and practical purposes.