How are directory structures stored in UNIX filesystem?

See file system internals which outlines in a rather simple way the internals of a typical Unix filesystem.

Most Unix filesystems contain

• A boot block
• A superblock (disk geometry, partition layout, inode count, etc)
• Inode blocks
• Data blocks

Modern filesystems contain additional structures.

One of the things in the superblock is the location of the inodes for the root directory.

A directory is a specially formatted file. As with all ordinary files, it has data blocks.

You can see this in The Linux Documentation Project: Filesystem

You can use debugfs to explore these structures.