Temporal variation in the population abundance of the deep-water rose shrimp, Parapenaeus longirostris (Lucas, 1846) (Decapoda, Penaeidae), and the Norway lobster, Nephrops norvegicus (Linnaeus, 1758) (Decapoda, Nephropidae), in the Tyrrhenian Sea (NW Mediterranean), were evaluated using time-series data (1994–2008) from experimental trawl surveys and commercial landings. The influence of several environmental variables (sea surface temperature, wind-mixing index and NAO index) and fishing effort indices (number of days at sea per month and mean engine power of the trawl fleet) were investigated. The time series were analysed by means of min/max auto-correlation factor analysis (MAFA) and dynamic factor analysis (DFA). The abundance of P. longirostris showed a clear increasing trend, significantly correlated with the fishing effort index (number of days at sea per month), the sea surface temperature and the wind-mixing index. The temporal variations in the stock of P. longirostris, which has a preference for warm waters, were positively correlated with the rise of the sea surface temperature and the decrease of wind circulation. For N. norvegicus, an increasing trend of landings per unit of effort and recruitment index contrasted with a decreasing trend of relative population abundance (biomass and density indices).