In Schizosaccharomyces pombe, a suppressor-active mutation at the anticodon site of the tRNASerUCA gene sup3 leads to opal (UGA)-specific suppression. Second-site mutations (rX) in sup3 inactivate the suppressor. The sup3-UGA, rX double mutants are genetically unstable in meiotic selfings, due to the intergenic transfer of information between sup3 and the unlinked genes sup9 and sup12 (Hofer et al. 1979; Munz and Leupold 1981; Munz et al. 1982). These three genes have considerable sequence homology over about 200 base pairs (Hottinger et al. 1982). Mutants showing a decrease or an increase of the meiotic instability at sup3 have been selected. One mutation (rec3-8) increases both the genetic instability and the frequency of intragenic recombination in sup3 by one order of magnitude. It has no effect on the stability of the nonsense alleles arg1-230 (UAA), ade6-704 and ural1-61 (UGA) or on the frequency of crossing-over between sup3 and the closely linked gene cdc8. The existence of a common genetic control over intragenic recombination and genetic instability at sup3 provides a direct way of selecting for rec mutants in homothallic haploid strains of S. pombe carrying a suppressor-inactive allele of sup3. It also supports the hypothesis that the instability of mutant alleles of this gene is due to chromosome mispairing at meiosis allowing sup3 to pair with sup9 or sup12 and then to undergo recombination by gene conversion restoring the suppressor-active allele sup3-UGA from the suppressor-inactive allele sup3-UGA, rX.(ABSTRACT TRUNCATED AT 250 WORDS)