Due to the lack of data on antimicrobial resistance patterns in Russian Helicobacter pylori clinical isolates, we aimed, for the first time, to comprehensively investigate resistance determinants in H. pylori isolates to metronidazole (MTZ) and levofloxacin (LVX) and to evaluate the correlation between genotypic and phenotypic antimicrobial susceptibility testing (AST). A retrospective analysis of 43 H. pylori clinical isolates from adult patients (2014-2022) was performed. Phenotypic AST was performed via the disk diffusion method. Total DNA was extracted using the QIAamp DNA Mini Kit. WGS of 43 H. pylori isolates was performed on the DNBSEQ-G50 sequencer. The phenotypic AST results revealed that 31 isolates were susceptible to LVX (LVX-S) and 11 were susceptible to MTZ (MTZ-S), while 12 were resistant to LVX (LVX-R) and 32 were resistant to MTZ (MTZ-R). To identify associations between phenotypic and genotypic resistance, a comprehensive analysis of nucleotide substitutions was performed in the following genes: gyrA, gyrB, rdxA, frxA, fdxB, and fur. Of all mutations identified in gyrA and gyrB, only D91G/N/Y in gyrA was associated with phenotypic resistance to LVX, being present in 4 of 12 (33.3%) LVX-R isolates (p<0.05). The combined mutation D91G/N/Y+N87K+A88P in gyrA was detected in 7 of 12 (58.3%) LVX-R isolates (p<0.001). No mutations in rdxA were associated with resistance to MTZ; however, 7 of 32 (21.9%) MTZ-R isolates had point mutations leading to a frameshift or premature termination of protein synthesis. Similarly, no mutations in frxA, fur, or fdxB were associated with resistance to MTZ. Based on the first results of whole-genome sequencing of Russian H. pylori clinical isolates, mutation D91G/N/Y was associated with phenotypic levofloxacin resistance. Despite the low frequency of point mutations N87K and A88P in gyrA gene, detection of the combined mutations D91G/N/Y+N87K+A88P may serve as a predictor of phenotypic resistance to levofloxacin in clinical isolates.