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<i>Sphagneticola trilobata</i> is an invasive plant in South China. A hybrid between <i>S</i>. <i>trilobata</i> and <i>Sphagneticola calendulacea</i> (a native related species) has also been found in South China. The drought resistance of <i>S</i>. <i>calendulacea</i>, <i>S</i>. <i>trilobata</i> and their hybrid was studied in this paper. Under drought stress, the leaves of <i>S</i>. <i>trilobata</i> synthesized more abscisic acid (ABA) than those of the other species to reduce stomatal opening and water loss. The activities of antioxidant enzymes were the highest in <i>S</i>. <i>trilobata</i> and the lowest in <i>S. calendulacea</i>. The leaves of <i>S. calendulacea</i> suffered the most serious damage, and their maximum photochemical efficiency was the lowest. RNA-sequencing ware used to analyze the expression levels of genes in ABA, antioxidant enzyme, sugar and proline synthesis and photosynthesis pathways. Further real-time PCR detection verified the RNA-sequence results, and the results were in accordance with the physiological data. The results showed that <i>S</i>. <i>trilobata</i> was the most drought tolerant, and the drought tolerance of the hybrid did not show heterosis but was higher than <i>S. calendulacea</i>. Therefore, compared with <i>S. trilobata</i> and the hybrid, the population number and distribution of <i>S. calendulacea</i> may be less in arid areas.