Novel Penicillium-like strains were isolated during the characterization of the mycobiota community dynamics associated with shrimp waste composting. Phylogenetic analysis of the partial β-tubulin (BenA) gene and the ribosomal DNA internal transcribed spacer region (ITS1-5.8S-ITS2) sequences revealed that the novel strains were members of section Lanata-Divaricata and were closely related to Penicillium infrabuccalum DAOMC 250537T. On the basis of morphological and physiological characterization, and phylogenetic analysis, a novel Penicillium species, Penicillium pedernalense sp. nov., is proposed. The type strain is F01-11T (=CBS 140770T=CECT 20949T), which was isolated from whiteleg shrimp (Litopenaeus vannamei) heads waste compost in the Pedernales region (Manabí province, Ecuador).