Amylose and resistant starch (RS) possess diverse health benefits besides serving as an important component in the starch industry. This study analyzed 48 subtropically-adapted maize inbreds at multiple locations and characterized for specific starch genes using markers specific to SNPs. Significant variation for amylose (0.3–66.4%), RS (1.8–38.0%), and total starch (65.5–75.1%) is observed. Amylose showed a positive correlation with RS (r = 0.79**). Molecular analysis using 29 markers produced 40 alleles with an average major allele frequency of 0.84. Gene diversity, polymorphism information content (PIC), and genetic dissimilarity are 0.23, 0.19, and 0.33, respectively. The genotypes are categorized into six major clusters based on the markers, and high amylose and RS lines are assigned to cluster-A and cluster-B. The alleles associated with Sbe2b (84 bp Del) and Sbe1a (SNP “A”) showed positive correlations with amylose and RS. Additionally, allele “A” linked to the Sucrose transporter6 (Sut6) displayed a positive correlation with RS. Considering Sbe2b, Sbe1a and Sut6 genes, six haplotypes are observed, of these, hap-A possessed the highest amylose and RS. The promising inbreds can be used as donors, while the validated markers for Sbe2b, Sbe1a and Sut6 genes can be effectively utilized for the improvement of amylose and RS through molecular breeding.