Instantaneous liquefaction of two-layer porous soil under nonlinear harmonic waves is presented. The governing equations are the poroelasticity equations accounting for the flow of pore water and the deformation of the soil skeleton yielding the coupled system. Possible simplifications to these equations are introduced in terms of including the inertial terms in the system. Finite element method is utilized for each formulation and the numerical results are first verified with their one dimensional analytical correspondents for the two-layer case. Then the problem of a two-layer plane strain soil system under waves in free field is studied in terms of instability of seabed defined through instantaneous liquefaction. Here both linear and non-linear waves are considered. A number of parametric studies are carried out to investigate the effect of wave non-linearity on the dynamic instability. The results indicate that instantaneous liquefaction of the two-layer system is affected by wave nonlinearity and is different from that of a single layer approach in free structureless field.