The RTPCR combined with RACE method was used to clone the complete cDNA sequence of ferredoxin gene (named as OnFd，GenBank accession No. KX461907) from Oncidium Kutoo ‘Litter Cherry’ (O.ornithorynchun × T. variegata). The complete cDNA sequence of OnFd was 989 bp，encoding 154 amino acids. Comparisons between the cDNA and genomic DNA sequences showed that intron was absent in OnFd. Bioinformatic analysis revealed that OnFd owns a typical ［2Fe2S］ domain. Blastp analysis showed that OnFd shares the highest similarity with Zea mays Fd3 (64.29%). Subcellular localization analysis indicated that the OnFd was located in the chloroplast. qRTPCR results showed that the expression level of OnFd was significantly higher in the flower than that in leaf and root，the lowest expression was found in pseudobulb. Moreover，we investigated the expression of OnFd in response to root rot pathogen infection in different tissues or organs. Result showed that the expression of OnFd accumulated quickly after pathogen infection，and very significant upregulation was found in pseudobulb at only 1 day post pathogen inoculation (dpi)(P<0.01)，The gene expression in plants from these five infected stages is 2.83-3.98 times than that of the healthy plants. The result suggested that the OnFd may play important role in Oncidiumsoft root pathogen interaction.