AbstractVitamin A deficiency is one of the major health problems worldwide. Traditional yellow maize possesses very low provitamin A (proA) concentration in endosperm. The influence of rare alleles of β‐carotene hydroxylase (crtRB1) and lycopene epsilon cyclase (lcyE) genes capable of enhancing proA concentration was studied in four BC2F2 populations generated using subtropical inbreds and CIMMYT‐HarvestPlus lines. The occurrence of severe segregation distortion for crtRB1 gene was observed, while lcyE gene was segregated as per Mendelian ratio. Genotype with favourable allele of crtRB1 (CC) had a significant effect on β‐carotene (BC) (7.9‐fold), β‐cryptoxanthin (BCX) (twofold) and proA (5.5‐fold) accumulation, compared to unfavourable genotype (C+C+). Genotype with favourable allele of lcyE (LL) showed 2.1‐fold, 1.6‐fold and twofold significant enhancement in BC, BCX and proA, respectively, over unfavourable genotype (L+L+) in pooled analysis. Of the nine genotypes, double homozygote (CC/LL) had the highest mean BC (12.60 μg/g), BCX (4.44 μg/g) and proA (14.82 μg/g), and combined effect was significantly better than individual gene effects or any other combinations. The information generated here would be useful in designing strategy for proA enrichment in subtropical maize.