Identifying connectivity patterns among remnant bird populations and their relationship with land use practices and subjacent habitat fragmentation is key for implementing appropriate management strategies for species conservation. The coastal thorn scrub forest and dune vegetation complex in the northern Yucatan Peninsula has been affected by coastal development. These human induced processes of land use change can affect the Yucatan Wren (Campylorhynchus yucatanicus), an endemic bird to this vegetation types with a narrow distribution. To identify possible anthropogenic barriers to connectivity of populations of C. yucatanicus, we collected 140 samples from 14 localities and used seven nuclear microsatellite loci to describe the current structure and genetic diversity of populations of C. yucatanicus. We explored the relationship between the genetic variability of populations and landscape structure through regression models. In addition, we described the relationship between genetic distance and landscape resistance. We found four genetic populations with Bayesian clustering methods. Human settlements and availability of adequate habitat limit the connectivity between sites due to ongoing land use changes. We suggest some management actions for conservation of this species, and we propose to change the IUCN threat category to "endangered" because of today the species has a more restricted distribution, small population, habitat degradation, loss of connectivity, and loss of genetic variability.