Background: Sea buckthorn (SBT) (Hippophae rhamnoides, L., Family Elaeagnaceae) is a small orange yellow-to-red–colored fruit, found on high altitudes in several Asian and European countries. SBT is referred to as “wonder plant” as seed oil is rich in Vitamins A, E, K, carotenoids, and phytosterols. SBT pulp is an excellent source of omega-7 fatty acids, while seed oil has high content of omega-3, 6, and 9 fatty acids. There are limited studies to evaluate its effects on periodontal pathogens. Objectives: (i) To evaluate the effect of SBT on clinical parameters (plaque index, gingival bleeding index, pocket depth, and clinical attachment level) in periodontitis patients. (ii) To evaluate the effect of SBT on microbiological parameters, i.e., anaerobic culture for Aggregatibacter actinomycetemcomitans (Aa) levels before and after nonsurgical therapy in chronic periodontitis patients. (iii) To compare the efficacy of SBT as an adjunct to nonsurgical therapy and nonsurgical therapy alone on Aa. Materials and Methods: A total of 24 patients were randomly allocated to control group (12 patients) that underwent scaling and root planing (SRP alone) and test group (12 patients) that underwent SRP along with intrasulcular SBT thixotropic solution delivery as local drug delivery (SRP + SBT). Clinical and microbial parameters are assessed at baseline and after 1 month. Results: The treatment modality used showed statistically significant improvement in both clinical and microbial parameters in test group compared to the control group. Conclusion: SBT was an effective adjunct in improving the clinical and microbial parameters compared to SRP alone in periodontitis patients.