Nitrogen-fixing bacteria have been isolated from sugarcane in an endophytic and beneficial interaction that promotes plant growth. In this work, for the first time, the involvement of ethylene signalling in this interaction was investigated by molecular characterizing members of this pathway in sugarcane. The expression pattern of a putative ethylene receptor (SCER1) and two putative ERF transcription factors (SCERF1 and SCERF2) show exclusive modulation in plants inoculated with the diazotrophic endophytes. The gene expression profile of SCER1, SCERF1, and SCERF2 is differentially regulated in sugarcane genotypes that can establish efficient or inefficient associations with diazotrophic micro-organisms, exhibiting high or low biological nitrogen fixation (BNF) rates, respectively. In addition, SCER1, SCERF1, and SCERF2 expression is different in response to interactions with pathogenic and beneficial micro-organisms. Taken together, that data suggest that SCER1, SCERF1, and SCERF2 might participate in specific ethylene signalling cascade(s) that can identify a beneficial endophytic association, modulating sugarcane responses toward the diazotrophic endophytes.