Maintaining gene flow among fragmented habitat patches is critical for the long-term persistence of wild species. Landscape genetics tools are often used to understand the impact of landscape features on gene flow among fragmented populations. The ability to detect the relationship between gene flow and landscape depends on the power of the genetic tools used, which increases with the number of genotyped loci. Next-generation sequencing (NGS) based methods allow genotyping of a high number of loci but are challenging to implement for non-invasive samples, which are commonly used in conservation genetics research. Here we assess the impact of landscape heterogeneity on jungle cat (Felis chaus) movement using genome-wide single nucleotide polymorphism (SNP) markers obtained from fecal samples, using a methylation-based DNA (MBD) enrichment method. We successfully genotyped 20 jungle cat individuals at 2246 SNP loci and compared our results to a previous study that used microsatellite markers and 93 individuals. Our results demonstrate the efficiency and robustness of the MBD enrichment approach with fecal samples in generating genome-wide data for endangered and cryptic species of conservation concern. Our landscape analyses revealed that roads and human-dominated land-use negatively impact jungle cat movement in central India. We explicitly quantified the uncertainty in our analyses and concluded that several thousand SNPs from fewer individuals provide more power than tens of microsatellites from more individuals, in quantifying the effects of landscape on gene flow. Our results provide insight into the impacts of anthropogenic habitat modification on an often-ignored small carnivore species. Insights on connectivity for such species can help policymakers and wildlife managers move beyond connectivity contingent on charismatic species to devise holistic landscape-level management plans for multiple carnivores.