To improve the analysis of unknown flanking DNA sequences adjacent to known sequences in nuclear genomes of photoautotrophic eukaryotic organisms, we established the technique of ligation-mediated suppression-PCR (LMS-PCR) in the green alga Chlamydomonas reinhardtii for (1) walking from a specific nuclear insertion fragment of random knockout mutants into the unknown flanking DNA sequence to identify and analyse disrupted genomic DNA regions and for (2) walking from highly conserved DNA regions derived from known gene iso-forms into flanking DNA sequences to identify new members of protein families. The feasibility of LMS-PCR for these applications was successfully demonstrated in two different approaches. The first resulted in the identification of a genomic DNA fragment flanking a nuclear insertion vector in a random knockout mutant whose phenotype was characterised by its inability to perform functional LHC state transitions. The second approach targeted the cab gene family. An oligonucleotide of a cabII gene, derived from a highly conserved region, was used to identify potential cab gene regions in the nuclear genome of Chlamydomonas. LMS-PCR combined with 3' rapid amplification of cDNA ends (3' RACE) and a PCR-based screening of a cDNA library resulted in the identification of the new cabII gene lhcb4. Both results clearly indicate that LMS-PCR is a powerful tool for the identification of flanking DNA sequences in the nuclear genome of Chlamydomonas reinhardtii.