Primitive cotton (Gossypium hirsutum L.) race stocks represent resources for genetic improvement for fiber quality, pathogen resistance, and increased tolerance to environment stresses. Most tropical primitive accessions are photoperiod sensitive and do not flower under the long days of U.S. cotton belt. The objective of this study was to identify QTLs related to time of flowering in an F2 population composed of 251 plants from the cross between Deltapine 61, a day neutral commercial cultivar and Texas 701, a photoperiod sensitive primitive accession. Simple sequence repeat (SSR) markers were used in molecular mapping of quantitative trait loci (QTLs) that are related to time of flowering of cotton. Five, five and four QTLs for node of first fruiting branch (NFB), node of first open boll (NOB), and flower number (FN), respectively showed additive effects by a mixed model approach based software-QTLMapper2.0. Two pairs of loci with additive × additive epistasis were detected for NOB, one pair of loci with additive × additive epistasis were detected for FN. The detected QTLs accounted for 28%, 36% and 37% of the phenotypic variations of NFB, NOB and FN, respectively. Interval mapping and MQM (multiple-QTL model) mapping by MapQTL5.0 were performed, further confirming the results of additive QTL loci. Selected determination of genotype using only the top and bottom 6% of the extreme phenotype was as effective as the entire population for detecting the most significant marker-trait associations.