Amoebiasis is an intestinal parasitosis caused by the protozoan Entamoeba histolytica that represents the third leading cause of mortality due to parasitosis. It is a prevalent disease in tropical climate regions with poor or absent sanitary services. Microscopy and antigen detection techniques are routinely used to diagnose amoebiasis because of their low cost and ease of application. However, these techniques do not differentiate E. histolytica infections and other potentially pathogenic species such as Entamoeba moshkovskii or Entamoeba bangladeshi. Therefore, in the last decades, molecular tests that allow correct identification of the causal agent of amoebiasis and the establishment of the prevalence of the infecting species have been developed. Techniques based on nucleic acids, such as conventional, multiplex, or real-time polymerase chain reaction (PCR), are being seriously considered in clinical laboratories, because they detect the etiologic agent directly from the sample without the need for previous prolonged culture, thus reducing diagnostic time. Also, the nested PCR test and the sequencing of ribosomal markers have allowed the identification of new parasitic species in humans, such as E. moshkovskii and E. bangladeshi, and an improved characterization of the known infecting species. The application of multiplex platforms allows the simultaneous identification of infecting species, increasing the sensitivity and specificity of these techniques. Therefore, the molecular diagnosis of amoebiasis is projected as an innovative tool in the fight against this parasitosis.