Conjugated linoleic acids (CLA) are health-promoting fatty acids found in foods derived from ruminant products that are formed in the rumen during bacterial biohydrogenation of linoleic acid (LA). Although selective antimicrobials might increase CLA production by manipulation of ruminal microflora, feeding of antibiotic growth promoters to livestock is declining due to fears of development of antibiotic resistance in human pathogens. This has initiated a search for alternatives, including plants containing bioactive compounds, which can have similar positive effects on ruminal microflora, but without negative impact on animal and human health. In this study we investigated effects of natural compounds in Australian plants on the bacteria and processes involved in ruminal biohydrogenation. Ethanolic extracts and essential oils were obtained from 91 Australian plants collected during 2004/2005 in Western Australia. Minimal Inhibitory Concentrations for the main bacterial species involved in rumen biohydrogenation were established using an agar dilution method, and effects of selected candidates on LA biohydrogenation was examined using an in vitro system with a mixed rumen bacterial population. A wide range of the plant extracts had selective inhibitory effect towards Clostridium proteoclasticum (which forms stearate from LA) without affecting Butyrivibrio fibrisolvens (which forms CLA and vaccenic acid, but not stearate). However, only a few plants, including Acacia iteaphylla and Kennedia eximia, inhibited LA metabolism or stearate formation in the mixed bacterial community in vitro. Further experiments are needed to investigate effects of selected candidates on CLA production in vivo.