GeneDiscoveR, a novel R package, facilitates gene discovery in plant traits via comparative genomics. Despite the advancements in plant genome sequencing technologies, gene discovery in model and even more in non-model plants remains challenging. To address this gap, we introduce GeneDiscoveR, which enables the identification of orthogroups linked to specific plant traits or treatment responses. Leveraging extensive genomic data from diverse plant lineages, for instance, liverworts, we showcase its efficacy in identifying trait-specific genes. OrthoFinder defines orthologs, while GeneDiscoveR statistically detects trait-associated orthogroups. Here, we applied GeneDiscoveR to liverwort genomes to find enriched orthogroups in species with oil bodies within specialized cells or with many oil bodies in all cells. Additionally, we used it to identify OGs related to self-incompatibility from Brassicaceae genomes. This bioinformatics pipeline offers insights into plant trait genetics, aiding future gene discovery endeavors.