The genus <em>Aeromonas</em> is present in a wide variety of water environments and is recognized as potentially pathogenic to humans and animals. Members of this genus are often confused with <em>Vibrio</em> when using automated, commercial identification systems that are culture-dependent. This study describes a PCR detection method for <em>Aeromonas</em> that is cultureindependent and that targets the <em>gcat</em> (Glycerophospholopid-Cholesterol Acyltransferase) gene, which is specific for this genus. The GCAT-PCR was 100% specific in artificially inoculated water samples, with a detection limit that ranged from 2.5 to 25 cfu/mL. The success at detecting this pathogen in 86 water samples using the GCAT-PCR method was identical to the conventional culturing method when a pre-enrichment step was carried out, yielding 83.7% positive samples. On the other hand, without a pre-enrichment step, only 77.9% of the samples were positive by culturing and only 15.1% with the GCAT-PCR. However, 83.7% positive samples were obtained for the GCAT-PCR when the water volume for the DNA extraction was increased from 400 μL to 4 mL. The proposed molecular method is much faster (5 or 29 h) than the culturing method (24 or 48 h) whether performed directly or after a pre-enrichment step and it will enable the fast detection of <em>Aeromonas</em> in water samples helping to prevent a possible transmission to humans.