[Description of methods used for collection/generation of data] A hybrid assembly approach was employed, integrating PacBio long-read sequencing with Illumina short-read data, an extensive functional annotation of the genome is provided by using AUGUSTUS with InterProScan and Sma3s., [Methods for processing the data] Software MaSuRCA and HASLR. Also Transdecoder to predict candidate coding regions., The sequencing of non-model species has increased exponentially in recent years, largely due to the advent of novel sequencing technologies. In this study, we construct the reference genome of the Spanish toothcarp (Aphanius iberus (Valenciennes, 1846)), a renowned freshwater fish species. A hybrid assembly approach was employed, integrating PacBio long-read sequencing with Illumina short-read data. In addition to the assembly, an extensive functional annotation of the genome is provided by using AUGUSTUS, and two different approaches (InterProScan and Sma3s). The integration of genomic data with predicted genes presents future research opportunities across multiple disciplines, such us physiology, reproduction, disease, and opens up new avenues for future studies in comparative genomic studies., PID2019-103936GB-C22, Project Aphanius., Annotation_Aphanius_iberus.xlxs, Peer reviewed