Late embryogenesis abundant (LEA) proteins, present in abundance in seeds during the late stages of development, are associated with desiccation tolerance. In the present work, we characterize a soybean LEA protein, GmPM16, with low molecular weight, high pI value, and an unusual amino acid residue distribution along the protein. The transcripts were detected in cotyledon mesophyll cells but not in the vascular system of mature or pod-dried soybean seeds. Circular dichroism (CD) analysis and Fourier transfer infrared (FTIR) spectroscopy indicated that the GmPM16 protein in solution was highly unordered, possessing only partial alpha-helical structures. However, the protein in sodium dodecyl sulfate (SDS) or trifluoroethanol (TFE) solution or in a dry state exhibited a conformation of abundant alpha-helical structures. As well, the GmPM16 protein interacts with sugar and forms tightly glassy matrixes in the dry state. The protein may play a role in reducing cellular damage in drying seeds by changing the protein conformation and forming tight cellular glasses.