Seabirds are of considerable conservation significance due to their key role in ecosystems and their generally high level of threat, especially from invasive species in breeding sites and as a result of bycatch during commercial fishing activities. We examined the genetic diversity, evidence for a bottleneck, and effective population size (N_e) of Red-billed Tropicbirds (Phaethon aethereus) from the Abrolhos Archipelago and White-tailed Tropicbirds (P. lepturus) from Fernando de Noronha Archipelago, both in the southwestern Atlantic Ocean. In addition, intraspecific genetic distance was assessed between 2 Red-billed Tropicbirds breeding on Fernando de Noronha and the larger population on Abrolhos, and between 5 White-tailed Tropicbird individuals breeding on Abrolhos and the breeding population on Fernando de Noronha, to identify relict populations. From 11 microsatellite loci, observed heterozygosity was 0.471 for White-tailed Tropicbirds and 0.267 for Red-billed Tropicbirds. Additionally, N_e was estimated to be as low as 100–200 individuals for each species, ∼25–50% of recent census estimates for the largest population of each species. No deviation from mutation-drift equilibrium was detected, but both species had M-ratios indicative of populations that had experienced a bottleneck or been recently established, and seem to have persisted as small populations over the past few centuries on both archipelagos. Small population size coupled with low evolutionary potential make these populations vulnerable to extinction. In our study sites and worldwide, tropicbirds show slow population growth and vulnerability to introduced predators. These species would benefit from both colony-based management and a better understanding of patterns of genetic diversity within and among populations.