Genes responsive to the environmental stresses which are retained after small scale duplication are part of plant genome duplication. However, information of duplicated genes that could be adaptive to environmental changes in plant is limited. This review presents an overview of duplication events in plant genomes which impact to gene duplication in relation to environmental changes, gene duplication as an adaptation mechanism, a case of duplicated nucleotide-binding site-leucinerich repeat (NBS-LRR) genes in soybean, and the gene duplication implementation for soybean plant breeding in Indonesia. Notably, genome duplication events generate gene duplication and contribute to adaptive evolution against environmental changes. Generalization of plants adaptation to the stressful conditions also probably improves our understanding of gene duplication as a mechanism of adaptation. Several recently duplicated NBS-LRR genes in soybean retain disease resistance QTL and the differential expression convince their contribution to biotic stress resistance in soybean. Proposed models of NBSLRR genes duplication process may help to understand these genes response to the environmental changes. The duplication of genes resistant to pest/disease, particularly NBS-LRR, provides important information for breeding parents selection and developing molecular markers related to desease resistance to genetically improve soybean in Indonesia. Overall, it may therefore be possible to enhance breeding programs which target on genes tolerant/resistant to biotic/abiotic stresses and provide a molecular basis for crop-stress protection strategy and improve soybean cultivars specified for harsh environment.