In 2021, Italy produced 23 thousand tons of Manila clam (Ruditapes philippinarum, Adam & Reeve 1850) from aquaculture, worth € 212 million, ranking as the world's second-largest producer. Production volumes of Manila clam have started to decline over the past 10 years due to, among other reasons, a decrease in the availability of wild seed on which clam farmers rely. This has led Italian clam farmers to buy seed from both national and foreign hatcheries. The Manila clam supply chain based on hatchery seed brings benefits to farmers, ensuring the continuity of production, but, on the other hand, production and environmental costs increase. As wild seed supply is expected to further decline due to climate change effects and habitat degradation, it is important to assess the environmental impacts of the actual production chains (conventional-wild seed and hatchery-based) to identify the hotspots and possible mitigation strategies. To this aim, this work applies the Life Cycle Assessment methodology to two case studies: a production chain based on wild seed, and, for the first time, a production chain based exclusively on seed produced in hatcheries. The results confirmed the general good environmental performance of mollusk aquaculture. For example, the Global Warming potential ranged from 0.85 to 1.05 kg CO2 eq kg−1 of clams, where the worst results refer to the production chain based on seed from the hatchery, as expected. Some production chain hotspots were highlighted: especially regarding the Global Warming potential, electricity consumption for the hatchery and depuration phases, and the use of fuels during the growth-out phase. Finally, scenario analysis has been applied to the worst-performing case study to understand the magnitude of the environmental benefits deriving from the adoption of some improvement strategies.