Exploring genetic diversity is crucial for effective breeding strategies to enhance crop performance under diverse environmental conditions and accelerate selection with improved yield and adaptability to climate change. This study aimed to explore the genetic diversity of eleven flax genotypes (Linum usitatissimum L.) using Start Codon Targeted (SCoT) markers and evaluate their performance in fibre yield contributing characters and seed yield-related traits in two field trials during 2021-2022 and 2022-2023 seasons. SCoT markers revealed varying degrees of polymorphism, with primers SCoT-1, SCoT-24, and SCoT-27 displaying 100% polymorphism, indicating high genetic diversity among the genotypes. Genetic similarity analysis categorized the genotypes into four diverse groups. The agronomic performance indicated that ‘S.620’, ‘Sakha 3’, and ‘S.651’ excelled in straw yield and associated traits such as technical length, plant height, fibre percentage, total fibre yield, fibre length, and straw yield, while ‘Sakha 5’ and ‘S.945’ showed the lowest. On the other hand, ‘Sakha 5’ followed by ‘S.933/15/2’ and ‘Sakha 6' were the top performers for seed yield and related characteristics, including fruiting zone length, number of capsules per plant, seed index, seed yield, oil percentage, and seed and oil yields, while ‘IV2’ exhibited the lowest values.