We report the effect of a thin GaN (2?nm) interlayer on the magnetotransport properties of AlInN/AlN/GaN-based heterostructures. Two samples were prepared (Sample A: AlInN/AlN/GaN and sample B: AlInN/GaN/AlN/GaN). Van der Pauw and Hall measurements were performed in the 1.9300?K temperature range. While the Hall mobilities were similar at room temperature (RT), sample B had nearly twice as large Hall mobility as sample A at the lowest temperature; 679 and 889?cm2/Vs at RT and 1460 and 3082?cm2/Vs at 1.9?K for samples A and B. At 1.910?K, the longitudinal magnetoresistance was measured up to 9?T, in turn revealing Shubnikovde Haas (SdH) oscillations. The carrier concentration, effective mass and quantum mobility of the two-dimensional electron gas (2DEG) were determined from SdH oscillations. At 1.9?K, the 2DEG concentration of sample B was nearly seven times larger than of sample A (1.67 x 10(13)/cm2 vs. 0.24 x 10(13)/cm2). On the contrary, the quantum mobility was changed adversely nearly three times (sample B 2500?cm2/Vs and sample A 970?cm2/Vs). The increase of the 2DEG concentration was attributed to the existence of the GaN interlayer, which has strengthened the spontaneous polarization difference between the AlInN and GaN layers of the heterostructure. Hence, the stronger electric field at the 2DEG region bent the conduction band profile downwards and consequently the quantum mobility decreased due to the increased interface roughness scattering.