INTRODUCTION: We aimed to describe the epidemiological situation during the Omicron variant circulation in light of genomic surveillance data in Martinique, a territory with low vaccination rates. PATIENTS AND METHODS: We exploited COVID-19 national databases of virological tests, for the collection of hospital data and for the sequencing data from December 13, 2021 to July 11, 2022. RESULTS: Three prevailing sub-lineages of Omicron have been identified in Martinique (BA.1, BA.2, BA.5) during this period causing three distinct waves characterized by an increase in virological indicators compared to previous waves, with moderate severity in the first and last waves, caused by BA.1 and BA.5, respectively. CONCLUSION: The SARS-CoV-2 outbreak is still progressing in Martinique. Genomic surveillance system in this overseas territory must be continued for rapid detection of emerging variants/sub-lineages.