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Combining ability studies have been extensively used to assess gene action responsible for various traits including disease resistance in maize. Some backcross (BC 3 F 2 ) and dihaploid (DH) lines developed through marker assisted selection have not been tested for their yield performances in hybrid combinations. A total of 16 BC 3 F 2 lines and their parental checks and 60 DH lines including lines and their parental checks were crossed to two single cross testers (CML312/CML442 and CML395/CML444) using Line x Tester design. The 152 three-way hybrids generated were evaluated for yield performance and other agronomic traits under artificial MLN inoculation, low nitrogen soil and optimum conditions in Kenya and South Sudan in 2019. Significant genotype, GxE, general combining ability (GCA) and specific combining ability (SCA) effects ( p ≤0.01) were detected for grain yield (t/ha) and maize lethal necrosis (MLN) scores. GCA effects were preponderant over SCA effects for most traits. High broad sense and moderate narrow sense heritability estimates for all traits across management options were detected. This implied that these traits could be improved through recurrent selection. DH lines D3, D14, D57 and BC 3 F 2 lines BCL3, BCL5, BCL8 showed desirable GCA effects for MLN resistance and grain yield. DH derived hybrids DH70, DH43, DH18 and DH40; and backcross (BC) derived hybrids BH28 and BH01 demonstrated desirable SCA effects for the same traits. Deployment of these MLN resistant lines into breeding programmes should result into improved MLN resistance and increased grain yields. The superior hybrids will provide desirable options for farmers who continue to experience low average maize yields due to MLN infections.