Seismic anisotropy of S-wave, trench-parallel or trench-normal polarization direction of fast S-wave, has been observed in the fore-arc and back-arc regions of subduction zones. Lattice preferred orientation (LPO) of elastically anisotropic chlorite has been suggested as one of the major causes of seismic anisotropy in subduction zones. However, there are two different LPOs of chlorite reported based on the previous studies of natural chlorite peridotites, which can produce different expression of seismic anisotropy. The mechanism for causing the two different LPOs of chlorite is not known. Therefore, we conducted deformation experiments of chlorite peridotite under high pressure–temperature conditions (P = 0.5–2.5 GPa, T = 540–720 °C). We found that two different chlorite LPOs were developed depending on the magnitude of shear strain. The type-1 chlorite LPO is characterized by the [001] axes aligned subnormal to the shear plane, and the type-2 chlorite LPO is characterized by a girdle distribution of the [001] axes subnormal to the shear direction. The type-1 chlorite LPO developed under low shear strain (γ ≤ 3.1 ± 0.3), producing trench-parallel seismic anisotropy. The type-2 chlorite LPO developed under high shear strain (γ ≥ 5.1 ± 1.5), producing trench-normal seismic anisotropy. The anisotropy of S-wave velocity (AVs) of chlorite was very strong up to AVs = 48.7% so that anomalous seismic anisotropy in subduction zones can be influenced by the chlorite LPOs.