The FecG^E allele of the ovine GDF9 gene, reported previously in the Santa Inés breed in Brazil, is segregating in Pelibuey, another hair type sheep breed in México. To determine allelic and genotypic frequencies, as well as effects on prolificacy and potential for marker assisted selection, 160 Pelibuey ewes from 4 flocks in different regions of México [Jalisco 1 (n = 34), Jalisco 2 (n = 62), Tabasco (n = 30) and Chihuahua (n = 34)] were genotyped by RT-PCR (StepOnePlus) using the FAMACTTCAAACAGTTTCTTTTTMGBNFQ and VICTCAAACAGTGTCTTTTTMGBNFQ probes (Applied Biosystems). Pearson’s Ji-squared was used to test genotypic frequencies for Hardy-Weinberg equilibrium. After discarding data of lambings that resulted from synchronized estrous with hormones, 631 records of the Poisson variable prolificacy were analyzed using a generalized linear model with PROC GLIMMIX of SAS (SAS Institute Inc., Cary, NC.). The model included fixed effects of year, season, flock, genotype, 2-way interactions and age as a covariate, as well as the random effect of ewe within flock and genotype. The average frequency of the FecG^E allele was 0.48 (0.48 to 0.54 for the flocks in Jalisco and Chihuahua, and 0.35 for the flock in Tabasco, which is in most challenging environment). Genotypic frequencies were as expected under Hardy-Weinberg equilibrium (P > 0.10). Back transformed estimated means for litter size for ewes of the different genotypes were 1.43 for +/+, 1.73 for +/E, and 1.78 for E/E (P < 0.05). For genotypes +/+, +/E, and E/E, frequencies of litters with more than 2 lambs were 0.5, 11.4, and 15.2%, respectively; frequencies of litters with a single lamb were 56.0, 37.6, and 35.6%, respectively. Homozygous E/E ewes reproduced normally, in agreement with results from Brazil, but in contrast to the sterility of homozygous ewes reported for other GDF9 mutations in European breeds. Potential for marker assisted selection exists, especially to produce homozygous rams to be used in low-prolificacy commercial flocks and(or) in crossbreeding with low-prolificacy well-adapted maternal breeds under harsh environments to obtain F₁ ewes.