In Estonian local mills, protein content (PC) and wet gluten content (WGC) are among the main indicators considered and evaluated when purchasing grains. Protein composition also significantly affects baking quality. The baking quality of ten winter wheat (WW) and spring wheat (SW) varieties was studied at the Center of Estonian Rural Research and Knowledge (METK). PC, WGC, gluten index (GI), and dough stability time (DST) were higher in SW varieties. PC was positively correlated with WGC and loaf volume (LV) in both wheat types. PC and WGC were negatively correlated with GI and positively correlated with DST only in WW. The viscoelastic properties of dough are linked to its high- and low molecular weight glutenin subunits (HMW-GS and LMW-GS). The allelic composition of the glutenin genes was determined using DNA markers. All the studied varieties had the allele Glu-D1d and additional allele Glu-D1a was found in the variety ‘Voore’. Fourteen varieties had Glu-A1a and b alleles associated with improved backing quality. Alleles Glu-B1с and Glu-B1b were found in WW varieties. SW varieties carried alleles Glu-B1al, b, с and h. The average QS was higher in SW. Eight varieties had null alleles Glu-A1c, Glu-A3e, and Glu-B3j, which negatively affected bread-making quality.