DArTseq silicoDArT and Single Nucleotide Polymorphism (SNP) markers (report DTi16-2108) and DArTcap SNP markers (report DTi17-2714_DTi17-2713). A Microsoft Excel file containing i) 21,195 SNP and 27,150 silicoDArT DArTseq genotypes and respective marker sequence and metadata information for 1404 tilipia (Oreochromis niloticus, O. mossambicus and hybrid) core breeding population samples; and ii) 1334 SNP DArTcap genotypes for 2057 Oreochromis niloticus hatchery samples. Corresponding .Rdata files containing genlight objects are also provided