Only a little information is available on the genetic association of basic within-boll yield components of segregating populations. A total of 25 genotypes were evaluated for genetic diversity using SSR markers in 2012; of these, eight diverse genotypes were selected to attempt the generation of five crosses. From the progeny of these five crosses, five F3 populations were developed. Data for within-boll yield components were recorded by taking 30 observations (one observation average of five bolls) from each population, and analysed for genotypic and phenotypic correlations followed by the path coefficient analysis from the genotypic correlation. The highest genotypic correlation was observed between seed cotton yield per locule and number of seeds per boll (ranging from 0.654 to 0.972 for different crosses). Except number of seeds per locule and lint percentage, all the other within-boll yield components had a highly significant positive correlation with seed cotton yield, whereas the former two had a negative correlation. Path coefficient analysis revealed that number of seeds per boll had a maximum direct effect on yield (ranging from 0.776 to 0.895 for different crosses), and also had a relatively high magnitude of the indirect effect via other traits. Differences were observed in the magnitude of correlation coefficients and direct/indirect effects for different populations, but the direction of genetic association always remained the same. The present study showed that number of locules per boll, seed cotton yield per locule, number of seeds per boll and seed cotton yield per boll can be used as efficient selection criteria for the improvement in seed cotton yield.