Marine sandy beaches are heterogeneous ecotones characterized by a complex mesh of environmental variables acting at different spatial scales. Arenicolous marine fungi are an ecological assemblage of sand-associated heterotrophs that inhabits sandy beaches. This group of fungi have evolved to cope with fluctuating beach conditions, displaying a cosmopolitan distribution. However, only a fraction of this diversity has been studied and spatial patterns and genetic diversity remain elusive. Herein, we analyzed arenicolous marine fungal diversity in sandy beaches using massive sequencing technologies to approach this gap in knowledge. Our results revealed a remarkable diversity presenting local divergent clusters. This baseline data paves the way towards to the integrative comprehension of intertidal ecology.