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Mangroves grow at the interface between land and sea in tropical and subtropical latitudes. This study investigated microtopographical conditions and differences in soil properties, mangrove forest structure and species composition. Forest structure was analysed using number of individuals, the number of stems, plant height and basal trunk diameter. We found significant differences in forest structure for four microtopographical conditions designated as Border condition (BO), Channel (CH), Permanent flooding (PF) and Temporary flooding (TF). We found that Langucularia racemosa and Rhizophora mangle were the dominant species in BO and CH while Avicennia germinans was the dominant species in TF. Ecological indices showed that R. mangle was the most important species in the CH and PF conditions. Structural differences were found among the microtopographic conditions where the mangroves were taller and denser at the channel site characterized by lower salinity (< 36 ppt). Rhizophora mangle was excluded from the TFcondition characterized by waterlogged and saline soils where the stress tolerant but stunted A. germinans was found. Mangrove forests respond to the arid environment in the eastern Baja California Peninsula by containing dense and shorter trees, thus differing from tropical areas where communities are composed of a mixture of species without a clear dominant.