Genotyping arrays based on single nucleotide polymorphisms (SNPs) provide a low-cost, high-throughput platform. The development of a SNP array that fully reflects the genetic diversity of maize (Zea mays L.) germplasm and is applicable to molecular breeding programs is desirable. In this study, we developed a MaizeGerm50K array comprising 50,852 SNPs selected from the resequencing data of 1604 maize inbred lines and other markers. A genome-wide association study using a landrace panel genotyped with the array permitted mapping of several known genes. We also verified a candidate gene, RNA-binding motif protein 24-like 1 (ZmRBM24L1), delaying flowering through overexpression lines. Genomic selection for yield and agronomic traits showed high prediction accuracy. The MaizeGerm50K array is thus a valuable genomic tool for maize genetic studies and breeding.