Background: Helicobacter pylori is a highly prevalent pathogen infecting more than half of the global population, with considerable geographic variation in its genetic characteristics and antibiotic resistance patterns. The EPIYA motifs of the CagA protein play a critical role in bacterial virulence; however, data on the association between CagA genotypes and antibiotic resistance remain limited in Mongolia. Aim: To determine the antibiotic resistance, CagA EPIYA patterns, and clarithromycin resistance-associated mutations of H. pylori strains in Mongolia, and to evaluate the agreement between phenotypic and molecular diagnostic methods. Materials and Methods: Gastric biopsy specimens were collected from 210 patients undergoing endoscopy and cultured for H. pylori. Antibiotic susceptibility to metronidazole, clarithromycin, amoxicillin, levofloxacin, and tetracycline was determined using the E-Test method according to EUCAST guidelines. CagA EPIYA patterns were analyzed, and clarithromycin resistance-associated mutations (A2142C, A2142G, A2143G) were detected using real-time PCR. Result: H. pylori was successfully cultured in 86 of 210 samples (41%), and 61 isolates were included in the final analysis. CagA-positive strains accounted for 86.9%, with a predominance of Western-type CagA (52/53), while only one East Asian-type strain was identified. Among Western-type strains, the ABC (58.5%) and ABCC (37.7%) patterns were most common. The highest resistance rate was observed for metronidazole (70.5%), followed by levofloxacin (50.9%). Clarithromycin and amoxicillin resistance were both 19.7%, whereas no resistance to tetracycline was detected. Multidrug resistance (≥2 antibiotics) was observed in 45.9% of isolates, and 14.8% showed resistance to ≥3 antibiotics. Clarithromycin resistance-associated mutations were detected in 21.3% of isolates, predominantly A2143G. The agreement between E-test and real-time PCR methods was excellent (κ=0.95, p<0.001). Conclusion H. pylori strains in Mongolia are characterized by a predominance of Western-type CagA, with ABC and ABCC as the most common subtypes. Notably, the AAABC and AAAAB subtypes were identified for the first time. High levels of antibiotic resistance, particularly to metronidazole and levofloxacin, as well as a substantial prevalence of multidrug resistance, highlight the need for region-specific treatment strategies. In Mongolia, H. pylori demonstrated the highest resistance to metronidazole, accompanied by a high proportion of multidrug-resistant isolates.