| Linkage Group | Locus /Gene Name | Probe, Gene or Gene Product | References | Accession # |
| XVIII | EST 925020F05 | EST | A. Grossman et al., unpublished results | BE442454 |
| XVIII | CYTC6 | cytochrome c6 | Hill et al. (1991) | M67448 |
| XVIII | S68 | pcf6-8 cDNA, upregulated after deflagellation | Schloss et al. (1984) | |
| XVIII | GP384 | random genomic fragment | This study | |
| XVIII | CNA35 | cDNA corresponding to EST AV622556 | This study | AV622556 |
| XVIII | CNC28 | cDNA fragment | This study | |
| XVIII | CLPK1 | cyclic nucleotide dependent protein kinase | U. Kawabata et al., unpublished results | AB042714 |
| XVIII | RAA2 | trans-splicing factor | Perron et al. (1999) | AJ243394 |
| XVIII | ODA1 | cDNA corresponds to EST BG854636 | Takada et al. (2002) | AY039618 |
| XVIII | ARS | arylsulfatase | De Hostos et al. (1989) | X52304 |
| XVIII | DHC8 | dynein heavy chain 8 | Porter et al. (1996) | U61371 |
| XVIII | CNB21 | cDNA corresponding to EST 833007B10 | This study | AW676519 |
| XVIII | J134 | genomic fragment | J. Jarvik, unpublished results | |
| XVIII | IDA7 | 140 kDa inner arm dynein | Yang and Sale (1998); Perrone et al. (1998) | AF159260 |
| XVIII | GP431 | random genomic fragment | This study | |
| XVIII | GP223 | random genomic fragment | This study | AF467708 |