Introgression is an important source of genetic variation for crop improvement and interspecific introgression lines are important resources for plant breeders to access novel alleles. In addition to combining alleles from diverse genotypes and creating novel allelic combinations, interspecific hybridization also provides the opportunity to study gene flow and transmission of chromatin between species. Experimental advanced-generation backcross populations contain individuals with genomic compositions resembling those resulting from natural interspecific hybridization. Individual members of such advanced-generation populations usually retain some genomic features of the donor parent while they most closely resemble their recurrent (backcross) parent. In this study, we developed a reciprocal set of advanced backcross populations using two elite cotton cultivars, Acala Maxxa (Gossypium hirsutum) and Pima S6 (G. barbadense) as parents and investigated these populations, segregating for a few chromosomal segments, for the nature and pattern of reciprocal chromatin transmission in interspecific crosses. Limited correspondence in genomic regions recalcitrant for donor chromatin between the two reciprocal populations suggested the effect of species background on the introgressed chromatin segments. Furthermore, we selected near-isogenic lines (NILs) containing only one chromosomal segment introgressed from the donor parent in the recipient genome in such a way that the donor segments in the recipient genome would combinedly tile most of the donor parent’s genome. A total of 399 and 423 NILs were selected in the Acala Maxxa and Pima S6 backgrounds, representing 78.72% and 71.48% of the Pima S6 genome and Acala Maxxa genomes respectively. These populations (both advanced backcross lines and NILs) were evaluated for six major fiber quality traits as well as for lint percentage and for five phenological traits. A total of 206 QTLs were identified for these traits, majority of which were small effect QTLs (i.e., explaining <10% of phenotypic variance) exemplifying the merit of these populations in identification of small-effect QTLs. Although some reciprocal QTLs were identified, limited reciprocity of majority of the QTLs in the two backgrounds shows strong influence of recipient genome, in addition to the combined consequences of epistasis, small phenotypic effects and imperfect coverage of donor chromatin in the recipient background.