<p>Urbanization is one of the main drivers of forest fragmentation and habitat loss on a global scale. This process jeopardizes biodiversity by interrupting gene flow, decreasing genetic diversity and causing local extinction. In addition, it facilitates the occurrence of synanthropic species in urban ecosystems. The <i>Nasutitermes corniger</i> (Blattodea: Isoptera: Termitidae) is a native neotropical termite species with a large geographical distribution in both natural and urbanized ecosystems across the Neotropical Region, and is an important pest in many South American cities. This study aimed to evaluate the genetic diversity of 30 <i>N. corniger</i> colonies in remnant natural forest patches inside João Pessoa’s metropolitan urban matrix region (Northeast Brazil). Thus, four individuals (soldiers) from three colonies in 10 remnant habitat patches (<i>N</i> = 120) were sampled, and subsequently, all the individuals were genotyped for four microsatellite loci. No reduction in genetic diversity was found due to the absence of population genetic structure and isolation by distance. However, moderate endogamy and heterozygous deficit in most subpopulations were observed, suggesting inbreeding. It is proposed that the maintenance of <i>N. corniger</i> genetic diversity in urbanized ecosystems is facilitated by its generalist diet, polydomous nesting behavior (polycalism), and facultative polygyny/polyandry during the colony maturation process. Thus, the high resilience of <i>N. corniger</i> and its permeability within the urban matrix present significant challenges to the effective planning of control and management strategies for its infestations in the medium and long term.</p>