The Chinese native cool-season perennial grass species Festuca sinensis Keng ex E.B.Alexeev exhibits frequent asymptomatic infections with an asexual Epichloë fungal endophyte. Six Festuca sinensis ecotypes were collected in different geographical locations. Endophyte-positive (E+) plants and corresponding endophyte-free (E–) plants of these six ecotypes were identified and then measured for shoot morphological characteristics including plant height, tiller number and biomass. Significant difference due to different host ecotype was observed in both E+ and E– plants. However, significant difference due to endophyte was observed in only one or two ecotypes. Concentration of endophyte-derived alkaloids and semi-quantitative endophyte colonisation in E+ plants were also evaluated. All E+ plants produced both lolitrem B and peramine alkaloids, and significant variation in alkaloid concentration due to host ecotype or endophyte genotype was observed. Analysis of semi-quantitative endophyte colonisation by using qPCR revealed significant differences between ecotypes. This suggested that host ecotype had large impacts whereas the endophyte had only a minor effect. The results showed that endophyte, host ecotype and their complex interaction affected performance of Festuca sinensis ecotypes.