Soybean genotypes are adapted to narrow bands of latitude due to photoperiod sensitivity. There are several photoperiod-sensitive loci (E1, E2, E3, E4, E5, E6, E7, E8). Determinate and indeterminate growth habits are controlled by a single locus. The objective of our research was to examine the effects of photoperiod sensitivity and growth habit alleles on seed yield and other agronomic characters using isogenic lines. Twenty 'Harosoy' isolines with 11 photoperiod-sensitive genotypes many with both indeterminate and determinate growth habits were grown in the field at Ottawa, ON, from 2003 to 2007. Maturity ranged from 97 to 127 days, and seed yield increased linearly with maturity until about 112 days when it plateaued. Determinate lines were always shorter than indeterminate lines of equivalent maturity. Seed yield was associated with plant height, maturity, seed sugar concentration, seed weight and lodging. Effects of alleles at individual loci, and additive and epistatic effects across multiple loci were examined. At a single locus, photoperiod-insensitive alleles produced isolines that matured 8-11 days earlier, yielded less, and had shorter plants with reduced lodging. In multiple loci analyses, additive effects explained most of the variation in agronomic characters since additive models with E1, E3, E4, E7 and Dt1 loci included compared well to additive plus epistatic models and genotype-based models. Variation in photoperiod sensitivity and growth habit alleles results in a range of maturity, with pleiotropic effects on seed yield and agronomic characteristics, and play an important role in providing adaptation across latitudes.