The aim of this study was to evaluate substitution of soybean meal with canola meal and measure its effects on rumen anaerobic fungal population in early lactation Iranian Holstein cows. From d 5 to 56 postpartum, cows were fed diets that were isoenergetic containing soybean meal (SBM; n=3) or canola meal (CM; n=3). Cows were housed in tie stalls and fed the total mixed ration two times a day to allow 5 to 10% orts (as-fed basis). Competitive PCR technique was used to evaluate quantitative difference of anaerobic fungal population within the rumen under the dietary groups. A universal PCR primer pair GAF (F): 5\'-GAG GAA GTA AAA GTC GTT AAC AAG GTT TG-3\' and GAF(R): 5\'-GAA ATT CAC AAA GGG TAG GAT GAT TT-3’ was used to amplify a specific region of 18S rDNA from anaerobic rumen fungal. Standard control DNA was constructed for use in the competitive PCR and was shown to amplify under the same reaction condition and with the same amplification efficiency as the target DNA. The relative intensities of PCR products were used to compare variety of fungal population under fed treatments. The signal intensity was quantified by ImageJ 1.29x and expressed in arbitrary units. The data was analyzed using the GLM procedure of SAS (2001) for a completely randomized design. The rumen fungal population was not impacted by diet but numerically was decreased in the CM compare with the SBM diet (34.79 and 35.12±1.87 arbitrary unit, respectively). The results of this study demonstrated that substituting soybean meal with canola meal in the early lactation cows had no apparent effect on the fungal population

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