Tapping panel dryness (TPD) is one of the main limiting factors for increasing the yield of natural rubber, and causes serious economic loss to the rubber production. In this research, the genes associated with TPD were identified by oligonucleotide microarrays hybridized with the latex from TPD and healthy rubber trees, and validated with RT-PCR method. The results from microarray analyses showed that 26 genes were differentially expressed between the TPD and healthy rubber trees. The 26 differentially expressed genes were classified into the following functional categories, rubber biosynthesis, programmed cell death, stress/defense response, metabolism of reactive oxygen species, DNA methylation, ubiquitin-proteasome pathway, cellular communication and signaling, and protein synthesis, process and transport, etc. In addition, the expression patterns of 12 differentially expressed genes randomly selected were further validated by RT-PCR analyses. This research laid foundations for identifying genes related to TPD on large scale and revealing the molecular mechanism of TPD in rubber tree.