A system and method for indexing and searching textual archives using semantic units such as syllables and morphemes. In one aspect, a system for indexing a textual archive comprises an AHR (automatic handwriting recognition) system and/or OCR (optical character recognition) system for transcribing (decoding) textual input data (handwritten or typed text) into a string of semantic units (e.g., syllables or morphemes) using a statistical language model and vocabulary based on semantic units (such as syllables or morphemes). The string of semantic units that result from a decoding process are stored in a semantic unit database and indexed with pointers to the corresponding textual data in the textual archive. In another aspect, a system for searching a textual archive is provided, wherein a word (or words) to be searched is rendered into a string of semantic units (e.g., syllables or morphemes) depending on the application. A search engine then compares the string of semantic units (resulting from the input query) against the decoded semantic unit database, and then identifies textual data stored in the textual archive using the indexes that were generated during a semantic unit-based indexing process.