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Background  Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species  Zingiber kawagoii  and  Z. shuanglongensis  was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of  in situ  ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses.    Results  Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in  Z. kawagoii  and no nucleotide substitution but only indels found in  Z. shuanglongensis . Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species,  Z. kawagoii  and  Z. shuanglongensis  were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in  Z. kawagoii  than in  Z. shuanglongensis  explains the more widespread distribution of  Z. kawagoii  in Taiwan.    Conclusions  Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5081-3) contains supplementary material, which is available to authorized users.

Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species