We focus here on two prevalent meanings of the word gene in research articles. On one hand, the gene, named here “molecular gene”, is a stretch of DNA that is transcribed and codes for an RNA or a polypeptide with a known or presumed function (as in “gene network'), whose exact spatial delimitation on the chromosome remains a matter of debate, especially in cases with alternative splicing, antisense transcripts, etc. On the other hand, the gene, called here “Mendelian gene”, is a segregating genetic unit which is detected through phenotypic differences associated with different alleles at the same locus (as in “gene flow”). We show that the “Mendelian gene” concept is still extensively used today in biology research and is sometimes confused with the “molecular gene”. We try here to clarify the distinction between both concepts. Efforts to delineate the beginning and the end of the DNA sequence corresponding to the “Mendelian gene” and the “molecular gene” reveal that both entities do not always match. We argue that both concepts are part of two relevant frameworks for explaining the biological world.