Bromochloromethane (BCM), a halogenated methane analogue, was evaluated for its anti-methanogenic activity in both batch and continuous fermentation systems. For batch fermentation, a roughage-based substrate was incubated with mixed rumen microflora for 24 h at two concentrations of BCM (5 and 10 μm). A 89–94 % reduction in methane was obtained in terms of volume and truly degraded substrate (TDS; P < 0·05). The partitioning factor (an index of efficiency of microbial protein production; expressed as mg TDS/ml net gas produced) increased from 3·55 to 3·73 (P < 0·05), while the acetate:propionate proportion decreased from 2·80 to 2·22 (P < 0·05). A complete inhibition of methanogens was associated with a 48 % decrease in Ruminococcus flavefaciens, a 68 % increase in Fibrobacter succinogenes and a 30 % increase in rumen fungi when quantified using qPCR. The continuous fermentation was carried out using the roughage-based substrate in four fermenters, two fermenters being control and the other two fed with BCM (5 μm) once in a day, for nine consecutive days. A persistent effect of BCM on methane reduction (85–90 %) was obtained throughout the study (P < 0·05) with no effect on gas production, SCFA production, acetate:propionate proportion, true degradability and efficiency of microbial mass synthesis (P>0·05). The complete inhibition of methane resulted in a significant decrease in R. flavefaciens and methanogens (P < 0·05) and an increase in fungal population (P < 0·05), while there was no effect on total bacterial and F. succinogenes populations (P>0·05). The batch fermentation confirms the anti-methanogenic activity of BCM, while the continuous fermentation indicates the persistency of this effect under in vitro conditions.