The molecular and hydration structures of ectoine (2-methyl-4-carboxy-3,4,5,6-tetrahydropyrimidine), which is one of the most important compatible solutes in halophilic and halotolerant microorganisms, were investigated for the first time via ab initio molecular orbital (MO) calculations. The electronic structure of ectoine was assumed to be a zwitterionic form, and possible stable molecular structures in the gas phase were searched by geometry optimizations. Two stable structures were obtained at the MP2/6-31G* level, and their stability were almost the same. One has the geometry in which the COO group is in axial position and the other in equatorial position. The transition state (TS) of proton transfer between the zwitterionic ectoine where the COO group is in equatorial position and neutral ectoine was obtained at the MP2/6-31G* level. However, the energy barrier of the proton transfer was sensitive to the basis sets used and disappeared at the MP2/6-31G**//MP2/6-31G* level, indicating that the zwitterionic ectoine should not be a stable structure in the gas phase. In addition, the SCRF treatments at the MP2/6-31G* level showed that, in aqueous solution, the energy barrier is sensitive to the cavity radii. The ectoine-water I:1 complexes were also calculated, and 10 stable structures were found. In the most stable complex, ectoine is hydrogen bonding to one water molecule both at the oxygen atom of the COO group and at the hydrogen atom of the NH group. The calculation of the ectoine-water 1:4 complex showed that four types of hydration occur simultaneously. However, the hydrogen-bonding pattern found in the four types of hydration showed that more than four water molecules could solvate to ectoine.