The causal agent of Fusarium wilt, Fusarium oxysporum Schlecht. f. sp. melongenae, produces a vascular disease of eggplant (Solanum melongena L.). Resistant germplasm with wide variation is essential for controlling this disease via breeding, and understanding the genetic background helps design breeding strategies. This study screened 36 S. melongena germplasm landraces and cultivars for Fusarium wilt resistance. Fusarium oxysporum is a particularly complex species comprised of several pathogenic strains arranged into groups called formae speciales, which pose a challenge to developing resistant plant varieties. Screening and selecting resistant plant sources could play an important role in developing resistant or tolerant plant lines. High Resolution Melting analysis coupled with Sequenced Characterized Amplified Region marker for fast screening and accurate identification of Fusarium wilt resistant eggplant has been developed. The method could be useful in breeding where great numbers of plants need to be tested during germplasm evaluation, and for single plant selection. Breeders could use these findings to choose Fusarium wilt resistant cultivars/landraces for their improvement.