We constructed genome probing microarrays (GPM) that are specific to 39 lactic acid bacteria (LAB) in an effort to monitor microbial diversity and biological activity during the fermentation of kimchi, a traditional Korean vegetable product known to contain various health-promoting and immunity-boosting factors. Metagenomes and metatranscriptomes extracted from periodically sampled kimchi soup were labeled, hybridized and comparatively analyzed using GPMs. Each metatranscriptome was prepared by subtracting 16S rRNA and 23S rRNA from the total RNA, and selectively synthesizing mRNA-specific cDNAs from the rRNA-subtracted samples. Metagenomic analysis revealed 23 LAB related to kimchi fermentation [defined as bacteria with more than a 1% average relative composition (ARC)]. Metatranscriptome analysis revealed that, with the exception of two microorganisms, all LAB probed in the microarray contributed to kimchi fermentation. Moreover, the relative compositions of the major LAB remained unchanged (there was less than a 1.5% difference between the maximum and minimum values) in our metagenome analysis, while our metatranscriptome analysis revealed significant differences in the relative compositions of major LAB during fermentation (relative compositions changed by 2.4% to 9.5%). These data indicate that microorganisms that are less abundant in the flora (those with less than a 5% ARC in the metagenomic analysis) also participated in kimchi fermentation with relatively high activities.