Here, we report the draft genome sequence of Citrobacter freundii AYS58, an endophyte isolated from the roots of a maize plant in Mafikeng, South Africa. The genome was 5,569,547 bp and exhibited a GC content of 50.5% and 5,904 genes, with 5,658 coding sequences, 3 rRNAs, 82 tRNAs, and 1 CRISPR.