On the basis of the joint analysis of transcriptome and proteome data, two small heat shock protein genes, PcHSP26.5 and PcHSP17.8, were cloned by RT-PCR using seedling leaves of Pugionium cornutum (L.) Gaertn., and analyzed by bioinformatics software. Nucleotides and encoded proteins were analyzed by Real-time PCR for the expression patterns of the 2 genes under high temperature, low temperature, NaCl stress, ABA stress and drought and rewatering stress. The open reading frames of PcHSP26.5 and PcHSP17.8 are 699 bp and 462 bp, respectively, encoding 282 and 153 amino acids, respectively, of which PcHSP26.5 contains an intron. The relative molecular masses of PcHSP26.5 and PcHSP17.8 are 26 480 and 17 490, respectively, and their theoretical isoelectric points are 6.36 and 5.99, respectively. They are hydrophilic proteins without transmembrane structure and signal peptide sites. Subcellular location prediction and phylogenetic tree analysis showed that PcHSP26.5 is mainly located in the mitochondria and belongs to the MII subfamily; while PcHSP17.8 is mainly located in the cytoplasm and belongs to the CI subfamily. The results of real-time fluorescent PCR showed that under high temperature stress, relative expression levels of PcHSP26.5 and PcHSP17.8 genes in Pugionium cornutum (L.) Gaertn. decreased after reaching the peak at 1 h; under low temperature stress, the relative expression level of PcHSP26.5 gene decreased after reaching the peak at 0.5 h, and the relative expression level of PcHSP17.8 gene was lower than the control within 0.5-12 h, and showed an upward trend at 24 h; under NaCl stress, relative expression levels of PcHSP26.5 and PcHSP17.8 genes decreased after reaching their peaks at 1 h and 3 h, respectively; under ABA stress, relative expression levels of the PcHSP26.5 and PcHSP17.8 decreased after reaching the peak at 2 h; under drought and rewatering stress, the relative expression levels of PcHSP26.5 and PcHSP17.8 genes reached their peak at 9 days of drought, and then declined after rewatering.