Objective: The aim of this study was to understand the transmission dynamics of the HIV-1 subtype B epidemic in French Guiana and the factors that shaped the expansion of major phylogenetic transmission clusters. Design: HIV-1 subtype B pol sequences with associated epidemiological data obtained from 703 treatment-naive patients living in French Guiana between 2006 and 2012, which correspond to 91% of all HIV cases diagnosed in that period, were employed in this study. Methods: Maximum likelihood and Bayesian methods were used to construct phylogenetic trees, identify transmission clusters and estimate intervals between successive infections. Statistical analysis was performed to evaluate epidemiological characteristics associated with cluster membership. Results: HIV-1 subtype B pol sequences from French Guiana were distributed in 10 large/medium transmission clades (LMTC, n > 10, 55%), 19 small transmission clades (STC, n = 3–8, 10%), 36 dyads (10%) or were nonclustered (25%). The rate of clustering did not differ by sex or clinical stage, but sex workers, crack-cocaine users, young individuals (15–20 years) and nationals or migrants from neighbouring South American countries were more likely to cluster within LMTC than individuals from other groups. We estimated that 53–63% of immigrants were infected after the arrival in French Guiana and that 50% of HIV transmissions within LMTC occurred during the first 2 years after infection. Conclusion: These findings reinforce the notion that high-risk sexual behaviours among young individuals and migrants (postmigration) combined with late HIV diagnosis are key drivers of onward dissemination of major HIV transmission clusters in French Guiana.