| Linkage Group | Locus /Gene Name | Probe, Gene or Gene Product | References | Accession # |
| II | PKA | protein kinase A | N. Wilson and P. Lefebvre, unpublished results | AV390434 |
| II | KLP1 | kinesin-like protein | Bernstein et al. (1994) | X78589 |
| II | GP15 | random genomic fragment | This study | |
| II | GP36 | random genomic fragment | This study | |
| II | GP130 | random genomic fragment | This study | |
| II | CNC17 | cDNA corresponding to EST 1031071E11 | This study | BI724441 |
| II | S641 | pcf 6-41cDNA, upregulated after deflagellation | Schloss et al. (1984) | |
| II | CPX1 | coproporphyrinogen III oxidase precursor | Quinn et al. (1999) | AF133671 |
| II | ALAD | porphobilinogen synthase | Matters and Beale (1995) | U19876 |
| II | DIC8 | genomic fragment | B. Williams and J. Rosenbaum, unpublished results | |
| II | RB60 | protein disulfide isomerase | Trebitsh et al. (2001) | AF036939 |
| II | GP226 | random genomic fragment | This study | |
| II | S6175 | pcf 6-175cDNA, upregulated after deflagellation | Schloss et al. (1984) | |
| II | LC1 | LC1, 22 kDa dynein light chain | Benashski et al. (1999) | AF112476 |
| II | S6135 | pcf 6-135cDNA, upregulated after deflagellation | Schloss et al. (1984) | |
| II | CNB8 | cDNA corresponding to EST 1024021G10 | This study | BG848462 |
| II | GP366 | random genomic fragment | This study | |
| II | GP225 | random genomic fragment | This study | |
| II | DHC4 | dynein heavy chain 4 | Porter et al. (1996) | U61367 |
| II | GSP1 | gamete specific protein 1 | Kurvari et al. (1998) | AF108140 |
| II | CNA72 | cDNA fragment | This study | |
| II | CNA45 | cDNA corresponding to EST BI724982 | This study | BI724982 |
| II | ZYMC16 | gene expressed in zygotes | Wegener and Beck (1991) | |
| II | RBCS2 | ribulose biphosphate carboxylase small subunit 2 | Goldschmidt- Clermont and Rahire (1986) | X04472 |
| II | DHC2 | dynein heavy chain 2 | Porter et al. (1996) | U61365 |
| II | GAS18 | gene expressed during sexual differentiation | Von Gromoff and Beck (1993) | |
| II | GP383 | random genomic fragment | This study | |
| II | S321 | pcf 3-21cDNA, upregulated after deflagellation | Schloss et al. (1984) | |
| II | YPTC4 | small G-protein | Dietmaier et al. (1995) | U13167 |
| II | CNA43 | cDNA fragment | This study |