The permeability behavior of Ariake clays has been investigated by constant rate of strain (CRS) consolidation tests with vertical or radial drainage. Three types of Ariake clays, namely undisturbed Ariake clay samples from the Saga plain, Japan (aged Ariake clay), clay deposit in shallow seabed of the Ariake Sea (young Ariake clay) and reconstituted Ariake clay samples using the soil sampled from the Saga plain, were tested. The test results indicate that the deduced permeability in the horizontal direction (kh) is generally larger than that in the vertical direction (kv). Under odometer condition, the permeability ratio (kh/kv) increases with the vertical strain. It is also found that the development of the permeability anisotropy is influenced by the inter-particle bonds and clay content of the sample. The aged Ariake clay has stronger initial inter-particle bonds than the young and reconstituted Ariake clays, resulting in slower increase of kh/kv with the vertical strain. The young Ariake clay has higher clay content than the reconstituted Ariake clay, resulting in higher values of kh/kv. The microstructure of the samples before and after the consolidation test has been examined qualitatively by scanning electron microscopy (SEM) image and semi-quantitatively by mercury intrusion porosimetry (MIP) tests. The SEM images indicate that there are more cut edges of platy clay particles on a vertical plane (with respect to the deposition direction) and there are more faces of platy clay particles on a horizontal plane. This tendency increases with the increase of one-dimensional (1D) deformation. MIP test results show that using a sample with a larger vertical surface area has a larger cumulative intruded pore volume, i.e., mercury can be intruded into the sample more easily from the horizontal direction (vertical plane) under the same pressure. Therefore, the permeability anisotropy of Ariake clays is the result of the anisotropic microstructure of the clay samples.