Agroforestry is the combination of agriculture and forestry on farms and agricultural lands. The primary goal is to create a healthy and harmonious symbiosis with forest trees and agricultural crops using conventional farming techniques. Agroforestry is highly beneficial as it is a sustainable food production method. The main advantage of planting trees in between crops is to prevent water runoff and soil erosion. Plants undergo several unfavorable conditions during their growth cycle. Such conditions include abiotic stresses like drought, temperature, scarcity of nutrients and high levels of salt in the soil. This adversely affects the yield and productivity of crops. Molecular markers play a significant role in identifying stress tolerant genes in many crops. This helps in enhancing crop production, yield and most importantly improving food and nutrition security. Thus, it helps in improving the income of farmers. In this article, we will be studying the use of molecular markers to improve Agroforestry. Molecular markers are the most effective tools for the analysis of gene tags, genetic variability, phylogenetic evaluation and improvement of new and exquisite cultivars. The markers used in tree improvement are RAPD (Random Amplified Polymorphic DNA), RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment length Polymorphism), SSR (Simple Sequence Repeats) or Microsatellites and SNP (Single Nucleotide Polymorphism). There are numerous advantages of using molecular markers in tree improvement as they been placed on the tree population, and it is been screened for a wide range of variety of physiological and quality traits. They play an important role in enhancing genetic gain for quantitative traits. With the help of molecular markers, they can do phenotyping, genotyping and also the construction on the tree populations. The selective markers are used to capture the extent of the genetic variation, as the diversity at the phenotypic level which is larger than the diversity at the marker level. Screening of controlled crosses in Neem tree, markers like M13, AP-PCR are used for germplasm identification; genetic mapping and breeding purposes are few among them. This project focuses on the molecular markers in tree improvement.