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<p>Abstract</p> <p>Background</p> <p>Polymorphisms of the mannose-binding lectin gene (<it>MBL2</it>) affect the concentration and functional efficiency of the protein. We recently used haplotype-specific sequencing to identify 23 <it>MBL2 </it>haplotypes, associated with enhanced susceptibility to several diseases.</p> <p>Results</p> <p>In this work, we applied the same method in 288 and 470 chromosomes from Gabonese and European adults, respectively, and found three new haplotypes in the last group. We propose a phylogenetic nomenclature to standardize <it>MBL2 </it>studies and found two major phylogenetic branches due to six strongly linked polymorphisms associated with high MBL production. They presented high Fst values and were imbedded in regions with high nucleotide diversity and significant Tajima's D values. Compared to others using small sample sizes and unphased genotypic data, we found differences in haplotyping, frequency estimation, Fu and Li's D* and Fst results.</p> <p>Conclusion</p> <p>Using extensive testing for selective neutrality, we confirmed that stochastic evolutionary factors have had a major role in shaping this polymorphic gene worldwide.</p>