Brucella abortus biovar 1 and atypical rough Brucella were isolated from Himalayan marmot (Marmota himalayana). Multiple-locus variable-number tandem-repeat analysis-16 typing indicated that the isolates both for smooth and atypical rough phenotypes had a common novel multiple-locus variable-number tandem-repeat analysis-16 type (Panel 1: 3-2-7-5-3-4-12-3; Panel 2A: 6-40-8; Panel 2B: 5-2-3-3-3).