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Meiotic recombination rates vary in response to intrinsic and extrinsic factors. Recently, heat stress has been shown to reveal plasticity in recombination rates in Drosophila pseudoobscura. Here, a combination of molecular genotyping and X-linked recessive phenotypic markers were used to investigate differences in recombination rates due to heat stress. In addition, haplotypes from the genetic crosses were compared to test if they deviated from equal proportions, which would indicate viability selection. To avoid this potential bias, SNP genotyping markers overlapping the regions assayed with mutant markers were used to further investigate recombination rate. Interestingly, skews in haplotype frequency were consistent with the fixation of alleles in the wild-type stocks used that are unfit at high temperature. Evidence of viability selection due to heat stress in the wild-type haplotypes was most apparent on days 7–9 when more mutant non-crossover haplotypes were recovered in comparison to wild type (p < 0.0001). Recombination analysis using SNP markers showed days 9–10 as significantly different due to heat stress in 2 pairs of consecutive SNP markers (p = 0.018; p = 0.015), suggesting that during this time period the recombination rate is most sensitive to heat stress. This peak timing for recombination plasticity is consistent with Drosophila melanogaster based on a comparison of similarly timed key meiotic events, enabling future mechanistic work of temperature stress on recombination rate.