The objective of the present study was to investigate the polymorphism of prolactin promoter and cytosolic phosphoenol pyruvate carboxykinase (PEPCK-C) intron 3 to exon 3 regions, and its association with economic traits in native fowl of Yazd province. These traits consisted of body weight at 8 (BW8) and 12 (BW12) weeks of age, age at sexual maturity (ASM), weight at sexual maturity (WSM), mean egg weight at 28, 30, and 32 weeks (MEW), and the number of eggs during the first 12 weeks of laying period (EN). Blood samples were collected from 159 pedigreed fowl at native fowl breeding center of Yazd province, and DNA was extracted from the samples according to saltingout protocol. PCR amplification together with restriction fragment length polymorphism was used to identify different genotypes of prolactin and PEPCK-C genes. The effect of prolactin genotypes on economic traits was analyzed using general linear model. A 24- bp indel (insertion or deletion) at nucleotide position (np) 358 was identified, but no polymorphism was found for PEPCK-C. Based on our results, the frequency of I and D alleles were 0.761 and 0.239, respectively. Frequencies of II, ID and DD genotypes were 0.566, 0.389 and 0.044, respectively. Genotypes II and ID were significantly associated with incresased EN (P<0.01). Meanwhile, the genotypes of the 24-bp indel site were not significantly associated with BW8, BW12, ASM, WSM and MEW (P> 0.05). The results of current study showed that using information of genes related to egg production could be used to improve the performance of native fowl of Yazd province.