Exon capture has emerged as a powerful and relatively cost-effective method for obtaining independently evolving nuclear loci, enabling robust phylogenetic inference across diverse taxonomic levels. While most exon capture studies have focused on resolving higher-level relationships, their potential for addressing species-level questions - particularly in refining and testing mtDNA-driven taxonomic hypotheses - is underexplored. In this study, we focus on a group of camaenid land snails endemic to the Australian Arid Zone. This genus, Catellotrachia, poses a challenge to conventional taxonomic approaches, because it comprises a series of morphologically similar species with supposedly highly restricted, yet primarily allopatric distributions. Using a published exon capture design that targets 500 orthologous nuclear loci to study deeper phylogenetic splits among the Camaenidae, here we assess the utility of these markers in resolving species-level relationships and even phylogeographic patterns to test current species hypotheses. In addition, we examine if often neglected intronic DNA can contribute to robustly resolving phylogenetic relationships. Our study proves that even a modest number of nuclear loci can effectively disentangle interspecific relationships and resolve species limits. However, the number of used markers and associated SNPs is relatively small limiting the ability to resolve the youngest splits confidently. We found that historical samples often contained rare genotypes, potentially misleading SNP-based phylogenetic analyses. We show that introns considerably increase the number of phylogenetically informative sites adding to the statistical support of phylogenetic inferences. Our findings highlight the applicability of exon capture to resolving fine-scale phylogenetic and taxonomic questions more generally.