Anaerobic rumen fungi (ARF) play an important role in the degradation of dietary plant cellulosic material. Subsequent decomposition products (mainly H₂ and CO₂) are utilized by other microbes, including methanogens. In the present study, we investigated the shift in ARF and methanogenic communities in dairy cows fed S1 diet (80% forage) 4 weeks before calving and moved to S2 diet (50% forage) after calving. Five cows from 2 study groups (SG: primiparous and multiparous) were sampled for ruminal contents before and after calving using a stomach tube. The genomic DNA from all rumen samples were amplified using archaeal and fungal specific primers, sequenced on a 454 Jr Roche platform and analyzed using QIIME pipeline. Approximately 18,317 and 35,582 reads were analyzed from 20 archaeal and ARF communities, respectively, resulting in 180 and 310 OTUs for archaea and ARF, respectively. Community comparisons (the Bray-Curtis distance matrix) revealed the effect of diet (P < 0.001) on ARF composition, while archaea communities differed between primiparous and multiparous cows (P < 0.05). Among ARF lineages, genus Cyllamyces was higher on S2 diet whereas, Cecomyces and Orpinomyces were higher on S1 diet, irrespective of parity. Methanobrevibacter showed >95% abundance across all samples. A co-occurrence analysis using dice index was performed, incorporating taxa from bacteria (published recently) and archaea and fungi from this study to determine the effect of diet and parity on inter-microbial relationships within the rumen. The co-existence patterns both within and between bacteria, archaea and ARF were more influenced by SG than by diets. In conclusion, the findings presented here indicate the influence of dry matter intake, stage of production and parity on rumen microbial communities.