The aim of the study was to investigate the differences of forestomach digestion and microbial communities between alpacas and sheep fed maize stalk-based diet. Six alpacas and six sheep were housed in metabolic crates, and were fed low-quality diet (30% maize-based concentrate and 70% rubbed maize stalk) twice a day. The animals were adapted to diet for 18 days, followed by 3 days of sampling. It was shown that alpacas had lower (P < 0.001) feed intake than sheep, but presented similar apparent digestibility in the total tract in comparison with sheep. The concentrations of propionate, valerate, isobutyrate and isovalerate in alpaca forestomach were higher (P < 0.001) than those in sheep, whereas acetate and acetate:propionate ratio was lower (P < 0.001) in alpacas than in sheep. The concentrations of ammonia-N and microbial protein in alpaca forestomach were 23 and 33% lower than those in sheep, respectively. For ruminal microbes, the proportions of fibrolytic bacteria Clostridium and Pseudobutyrivibrio were higher (P < 0.05) in alpacas than those in sheep, but the proportion of proteolytic bacteria Selenomonas was lower (P < 0.05) in alpacas. In conclusion, the forestomach fermentation characteristics in alpacas and sheep fed low-quality maize stalk diet were significantly different, and this phenomenon may result from the different composition of ruminal microbes (such as carbohydrate degrading bacteria and proteolytic bacteria).