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SNAREs (soluble N-ethylmaleimide-sensitive-factor attachment protein receptors) are engines for almost all of the membrane fusion and exocytosis events in organism cells. In this study, we identified 84 <i>SNARE</i> genes from banana (<i>Musa acuminata</i>). Gene expression analysis revealed that the expression of <i>MaSNARE</i>s varied a lot in different banana organs. By analyzing their expression patterns under low temperature (4 °C), high temperature (45 °C), mutualistic fungus (<i>Serendipita indica</i>, Si) and fungal pathogen (<i>Fusarium oxysporum</i> f. sp. <i>Cubense</i> Tropical Race 4, <i>Foc</i>TR4) treatments, many <i>MaSNAREs</i> were found to be stress responsive. For example, <i>MaBET1d</i> was up-regulate by both low and high temperature stresses; <i>MaNPSN11a</i> was up-regulated by low temperature but down-regulated by high temperature; and <i>Foc</i>TR4 treatment up-regulated the expression of <i>MaSYP121</i> but down-regulated <i>MaVAMP72a</i> and <i>MaSNAP33a</i>. Notably, the upregulation or downregulation effects of <i>Foc</i>TR4 on the expression of some <i>MaSNAREs</i> could be alleviated by priorly colonized Si, suggesting that they play roles in the Si-enhanced banana wilt resistance. <i>Foc</i> resistance assays were performed in tobacco leaves transiently overexpressing <i>MaSYP121</i>, <i>MaVAMP72a</i> and <i>MaSNAP33a</i>. Results showed that transient overexpression of <i>MaSYP121</i> and <i>MaSNPA33a</i> suppressed the penetration and spread of both <i>Foc</i>1 (<i>Foc</i> Race 1) and <i>Foc</i>TR4 in tobacco leaves, suggesting that they play positive roles in resisting <i>Foc</i> infection. However, the transient overexpression of <i>MaVAMP72a</i> facilitated <i>Foc</i> infection. Our study can provide a basis for understanding the roles of <i>MaSNAREs</i> in the banana responses to temperature stress and mutualistic and pathogenic fungal colonization.