<p>The change in land use caused by anthropogenic processes is probably the main driver of biodiversity loss across terrestrial ecosystems. In Brazil, the Atlantic Forest is currently distributed in small remnant patches, mostly in small and isolated forest fragments that harbor a disproportionately high share of global biodiversity. Urbanization causes biodiversity loss worldwide, but there is a lack of knowledge regarding its effects on the genetic diversity of tropical rainforest organisms. We aimed to evaluate whether the urban matrix of João Pessoa is permeable and, if so, to assess its influence on gene flow and genetic diversity between and within termite populations from different feeding groups sampled in four Atlantic Forest fragments. We used four nuclear DNA microsatellite markers. From 36 colonies, we sampled four individuals (<i>N</i> = 144) among three termite species: <i>Anoplotermes banksi</i> (soil-feeder), <i>Embiratermes neotenicus</i> (wood–soil interface feeder), and <i>Nasutitermes corniger</i> (wood-feeder). Our study indicated maintenance of gene flow among forest remnants, which was unrestricted for <i>N. corniger</i>, showed low restriction (with private alleles) for <i>E. neotenicus</i>, and moderate restriction for <i>A. banksi</i>, with 20% of genetic distance explained by geographical distance between fragments. For termites, the configuration of the urban matrix contributes to functional connectivity, facilitating gene flow between forest remnants. The functional connectivity described for the three termite species in the studied urban landscape, with green patches distributed throughout the city, can be extended to other taxonomic groups, underscoring the importance of studies from this perspective for planning urban expansion strategies that ensure the conservation of green areas.</p>