Microalgae constitute an underexploited feed resource for ruminant nutrition. The unique digestive tract of ruminants makes them best suited to utilise complex polysaccharides and non-protein nitrogen of eukaryotic microalgae, though contrasting effects on rumen fermentation have been reported. The current study aimed to assess the effects of microalgae species, inclusion level and basal substrates on in vitro rumen fermentation parameters. To this end, haylage and maize silage were supplemented with 2.5, 5 and 10% (w/w, dry matter basis) of Chlorella vulgaris, Nannochloropsis oceanica and Tetraselmis sp. and incubated for 24-h with rumen inocula non-adapted to microalgae. No significant interaction was observed among basal substrate, microalgae species and inclusion level for any of the parameters evaluated. Substrate and microalgae species interaction affected most fermentation parameters. The lowest gas and methane productions and yields, total volatile fatty acids (VFA) production and concentrations of acetic, butyric and most minor VFA observed when C. vulgaris was incubated with haylage suggest that rumen fermentation was inhibited to a greater extent by this microalgae, probably reflecting a low availability of rapidly fermentable carbohydrates due to differences in cell wall structure and composition. However, the opposite was observed when C. vulgaris was incubated with maize silage, suggesting an improvement in the synchrony between fermentable energy and degradable nitrogen. Microalgae species and inclusion level interaction mainly affected methanogenesis. The lowest methane yield with N. oceanica at 10% may be explained by its high content of polyunsaturated fatty acids. The interaction between basal substrate and microalgae inclusion level did not affect any parameter. Overall, the effects of the interactions between substrate and microalgae species and microalgae species and inclusion level, underpin the importance of identifying optimal microalgae species and inclusion levels according to the basal diet fed to ruminants.