| Linkage Group | Locus /Gene Name | Probe, Gene or Gene Product | References | Accession # |
| III | CNC24 | cDNA fragment | This study | AF525918 |
| III | DHC a | dynein heavy chain alpha | Mitchell and Brown (1994,1997) | L26049 |
| III | EST 925021G06 | EST | A. Grossman et al., unpublished results | BE442506 |
| III | LRG5 | gene involved in blue light signaling | Glockner and Beck (1997) | U73818 |
| III | COX2A | cytochrome c oxidase subunit II | Perez-Martinez et al. (2001) | AF305080 |
| III | GSAT | glutamate-1-semialdehyde aminotransferase | Matters and Beale (1994) | U03632 |
| III | SAC1 | sulfur limitation gene | Davies et al. (1996) | U47541 |
| III | PF15 | component of the central pair microtubule apparatus | E. F. Smith and P. Lefebvre, unpublished results | |
| III | MAA7 | tryptophan synthase beta-subunit | Palombella and Dutcher (1998) | AF047024 |
| III | CNB4 | cDNA corresponding to EST 833013E07 | This study | AW721386 |
| III | GP108 | random genomic fragment | This study | |
| III | GP219 | random genomic fragment | This study | |
| III | EF12E | genomic fragment | E. Fernandez, unpublished results | |
| III | GAR1 | gamete activation regulated cobalamin-independent methionine synthase | Kurvari et al. (1995) | U36197 |
| III | NAP | novel actin-like protein | Kato - Minoura et al. (1998) | U68060 |
| III | NIT2 | NIT2 gene | Schnell and Lefebvre (1993) | |
| III | RIB43A | microtubule ribbon protein | Norrander et al. (2000) | AF196576 |
| III | FLA14 | LC8, 10 kDa dynein light chain | King and Patel-King (1995b); Pazour et al. (1998) | U19490 |
| III | AC208 | apoplastocyanin | Quinn et al. (1993) | L07282 |
| III | CPC1 | central pair-associated complex 1 protein | Mitchell and Sale (1999) | |
| III | CNC21 | random cDNA fragment | This study | |
| III | PTX2 | phototaxis-deficient gene | Pazour et al. (1995) | |
| III | YPTC6 | YPTC6, small-G protein | Dietmaier et al. (1995) | U13169 |
| III | LC6 | LC6, 13 kDa dynein light chain | King and Patel-King (1995b) | U19484 |
| III | UNI3 | delta-tubulin | Dutcher and Trabuco (1998) | AF013108 |
| III | TUA1 | alpha1-tubulin | Silflow et al. (1985) | M11447 |
| III | GP201 | random genomic fragment | This study | |
| III | GP317 | random genomic fragment | This study | |
| III | GP32 | random genomic fragment | This study | |
| III | CNA34 | cDNA corresponding to EST 1031065B08 | This study | BI722955 |
| III | GP437 | random genomic fragment | This study | |
| III | RSB1 | radial spokehead polypeptide 1; corresponds to EST 1031064E02 | Williams et al. (1986); this study | BI722838 |
| III | PHOT1 | phototropin-like protein | K.Y. Huang, T. Merkle, and C.F. Beck, unpublished results | AJ416557 |