<p><i>Terminalia bellirica</i> (Gaertn.) Roxb. is a medicinally important tree species currently experiencing population decline in northern India. However, baseline information of conservation relevance such as genome sequence data, molecular marker resources, and population-level genetic insights, is lacking. The present study aimed to develop de novo simple sequence repeat (SSR) markers and utilize them for population genetic analysis. Using a shallow-pass genome sequencing approach with the Illumina platform, approximately 52.86 million raw reads were generated. A truncated genome assembly of 168.6&#xa0;Mb was obtained and screened for the presence of SSRs. In total, 66,015 SSRs were identified, and 21,855 primer pairs were designed for amplification. After validation, nine polymorphic SSR markers were identified and used to evaluate 15 populations of <i>T. bellirica</i> collected from northern India. The SSR primers exhibited adequate polymorphism, with a mean polymorphism information content (PIC) value of 0.63. The studied populations of <i>T. bellirica</i> exhibited a high level of genetic diversity, as reflected by the mean values of expected heterozygosity (He = 0.65), observed heterozygosity (Ho = 0.65), and allelic richness (Ar = 20.98). Most of the total genetic variation (97.35%) was found within populations, and the fixation index was very low (F_ST = 0.02), indicating negligible genetic differentiation among populations. This pattern was further supported by the absence of significant clustering and weak population genetic structure. While genetic parameters suggest that the populations are currently stable, the genetic information generated herein serves as valuable baseline data for guiding future conservation strategies for <i>T. bellirica</i>. To the best of our knowledge, this study presents the first comprehensive set of de novo SSR markers and insights into the population genetic structure of <i>T. bellirica</i>.</p>