To increase our understanding of the impact of land use/cover changes on the diversity of soil microbial functional genes in microbial communities, we analyzed soil samples of fir old growth forest (Abies faxoniana) and planted spruce forest (Picea likiangensis var. balfourianan) in 1960s following the harvest of the old growth forest samples were collected from the Miyaluo forest in a subalpine area of Western Sichuan and were analyzed using a functional gene microarray. This type of functional gene microarray contained 1961 probes complementary to gene orthologs from six functional groups: organic carbon decomposition, carbon fixation, metal resistance, and nitrogen, sulfur, and phosphorous cycling. A total of 39 and 62 genes with statistically significant positive signals (SNR≥2) were observed in fir old growth forest and planted spruce forest in 1960s, respectively. The gene diversity index (H′) was 3.59 and 4.04 and the observed sum signal intensity was 480280 and 630560 in fir old growth forest and planted spruce forest in 1960s, respectively. There were 32 and 37 organic carbon decomposition genes that accounted for 82% and 60% of all observed genes in fir old growth forest and planted spruce forest in 1960s, respectively. These organic carbon decomposition genes belonged to 22 different orthologs that are involved in a variety of organic carbon decomposition process, such as decomposition of lignin, xylan, chitin. However, the individual gene orthologs associated with organic carbon decomposition and their abundance were diverse in these sites. For example, the benzoyl CoA reductase gene related to benzoate decomposition, originally found in Azoarcus evansii, was the most abundant in these sites. The putative 2-hydroxychromene-2-carboxylate isomerase gene from Ralstonic solanacearum was only observed in spruce forest planted in 1960s and had highest abundance among all the detected genes. These results showed that most soil microbes may directly take part in the decomposition of soil organic carbon and differences in forest types can significantly affect the microbial community structure and the molecular diversity of organic carbon decomposition genes. Therefore, land use/cover changes may have a large influence on the soil microbial community structure and the microorganisms involved in organic carbon decomposition. This in turn likely affects the organic carbon cycle dynamics and the increase in atmospheric CO₂ concentration. In addition, the results also indicated that the developed microarray appeared to be useful for analyzing differences in functional microbial community structures.