Fermented foods are considered as an integral part of the global human diet. Fermented foods also have unique microbial communities such as bacteria, archaea, fungi, and viruses that are essential to the fermentation process and affect final product characteristics. Despite the ecological importance of virus, little is known about the diversity and ecological role of virus in the food ecosystem. In this study, the viral and host bacterial communities from 10 representative samples of Korean and Chinese kimchi were analyzed in triplicate using next-generation sequencing technology. The overall structures of bacterial and viral communities were dominated by lactic acid bacteria in phylum Firmicutes and bacteriophages in order Caudovirales, respectively. For the single-stranded DNA (ssDNA) viruses, bacteriophage in family Microviridae were dominant in Korean kimchi. After correction for multiple comparisons using false discovery rate (FDR, P < 0.05), the relative abundances of 6 bacterial taxa and 33 viral host taxa at the genus level were significantly different between Korean and Chinese kimchi. Notably, in beta-diversity analysis, viral communities were much more clearly separated according to their geographical origin (PERMANOVA pseudo-F = 11.57, P < 0.001 in Bray–Curtis PCoA) than bacterial communities (pseudo-F = 4.75, P < 0.001 in unweighted UniFrac PCoA). Thus, viral metagenomics represents a potentially useful in-depth analytical method for determining the geographical origins of fermented foods.