Hibiscus tiliaceus L. is a mangrove associate that occupies the divergent environments of intertidal wetland (L population) and inland (T population). Thus, it is an ideal plant for the study of ecological adaptation and salt tolerance. In this study we compared responses of the two populations to salinity combining a global transcriptional analysis and physiological analysis. Microarray transcript profiling analysis showed both shared and divergent responses to salinity stress in the two populations. A total of 575 unigenes were identified as being salt-responsive in the two populations. Shared responses were exemplified by the regulated genes functioning in confining ribosomal functions, photosynthesis and cellular metabolism. A set of genes functioning in cellular transporting and cell detoxification and a crucial transcription factor AP2 domain-containing protein involved in environmental responsiveness, were differently expressed in the two populations. Physiological analysis showed that the L population was less susceptible to salt stress in photosynthesis and had a stronger capability of K+:Na+ regulation than the T population. Both microarray and physiological data showed the L population possess higher fitness under high salinity, probably due to it its long-term adaptation to their native environment.