Sugarcane (Saccharum spp. hybrids) is a prominent cash crop that produces 78% of the global sugar production and is widely utilized for biofuel production. Due to its highly heterozygous genome, which has a high frequency of polymorphisms, and an extended breeding cycle that spans up to 10–15 years, typical breeding methods are problematic to use. Remarkably, all major producing countries in the world have selected and bred new varieties and continuously upgraded them as a solid guarantee to promote the steady development of the sugarcane industry. The key aspects of the selection process focus on traits such as high-sucrose content, strong resistance to diseases such as red rot, smut, brown rust, and leaf scald, low flowering propensity, and robust ratooning ability. The development and utilization of wild germplasm is very limited in the case of sugarcane; consequently, breeding technology in sugarcane cultivation is lagging compared to crops such as rice, maize, and soybeans. In this context, molecular markers have emerged as a transformative tool in modern plant breeding, offering unprecedented precision and efficiency in developing improved sugarcane varieties. The utilization of molecular markers was popularized in plant breeding in the era of breeding 3.0, along with techniques such as transgene, gene editing, and genomic selection to develop new varieties by selecting or aggregating the key regulating genes. Molecular markers, including various types such as RFLP, SSR, and SNP, have transformed how breeders approach the genetic enhancement of crops. Molecular markers have played a crucial role in identifying genetic polymorphism linked with desirable agronomic traits, enabling precise and effective selection. Selection and planting of desired trait-bearing varieties, such as prevalent disease-resistant varieties are one of the cost-effective and practical strategies for developing sugarcane varieties with desired qualities. To enhance this process, molecular-assisted selection breeding is adopted, offering a reliable and effective method that is usually minimally affected by peripheral environmental factors. Recently, methods like high-throughput sequencing and genotyping have improved the capability to identify and use molecular markers. Diversity array technology (DArT), which uses a high-yield microarray platform to cover the whole genome and identify hundreds of thousands of polymorphic markers in a single study, could be a viable large-scale approach. Bulked segregant analysis (BSA) combined with molecular marker analysis of quantitative trait loci has proven effective in developing genetic maps around resistance genes in sugarcane, aiding in the fight against diseases and pests. Similarly, integrating omics data with molecular markers could offer even more significant advantages in the breeding field by predicting the breeding value of complex traits and thus enhancing the development of superior varieties. Despite these molecular markers incorporated in breeding approaches, they face several difficulties, such as high cost, resource requirements of molecular marker programs, and genome complexity. However, integrating artificial intelligence and machine learning will further boost the ability to elucidate complicated genetic information, driving the development of next-generation sugarcane varieties. The ongoing advancements in molecular marker technologies will ultimately determine the future of sugarcane breeding.