Abstract Background The European sardine ( Sardina pilchardus Walbaum, 1792) has a high cultural and economic importance throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Consequently, there is an urgent need to better understand the causal factors of this continuing decrease in the sardine stock. Important biological and ecological features such as levels of population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources. Findings The sardine genome of a single female individual was sequenced using Illumina HiSeq X Ten 10X Genomics linked-reads generating 113.8 Gb of data. Three draft genomes were assembled: two haploid genomes with a total size of 935 Mbp (N50 103Kb) each, and a consensus genome with a total size of 950 Mbp (N50 97Kb). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of eleven tissues were sequenced and used to aid the functional annotation of the genome, resulting in 40 777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of more than 2.3 million phased SNPs with heterozygous loci. Conclusions A draft genome was obtained with the 10X Genomics linked-reads technology, despite a high level of sequence repeats and heterozygosity that are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data are a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.