Hybrid resequencing using HiSeq and PacBio technologies of the antibacterial innate immune genes coding for toll-like receptors, namely TLR1, TLR2, TLR4, TLR5, and TLR6, in Czech Red Pied cattle (Czech Simmental) allowed us to determine haplotypes formed by the polymorphisms present. Directly determined haplotypes in the range of the large proximal amplicon in TLR2 formed two clusters in the network tree graph. Consistently, the distribution of the statistically reconstructed haplotypes was similar both in TLR2 and in other TLRs. Only the limited diversity of TLR1 did not allow for any assumption. The stability of this phenomenon cannot be ascribed to the historical origin but rather to a long-term effect of balancing selection. The equilibrium might be based on two different essential functions performed by the TLR genes or their products. The formation of two kinds of heterodimers by the TLR2 product, namely, TLR2/TLR1 and TLR2/TLR6 with different ligand specificities, is considered to be a particular case.