We derive ugri photometry of ~1.7 million sources over the ~21 square degree area of the Fornax Deep Survey (FDS) centered on the bright galaxy NGC1399 (fds.dat). For a wider area, of ~27 square degrees extending in the direction of NGC1316, we provide gri photometry for ~3.1 million sources (fdsex.dat). The identification of compact sources, globular clusters (GC) and ultra compact dwarf galaxies (UCD), is obtained from a combination of photometric and morphometric selection criteria taking as reference the properties of confirmed GCs and UCDs in the literature. The master tables of GC and UCD are also provided. <P />(4 data files).