Stocks with low market value are rarely included in stock assessments because their catch records are generally lacking, thus adding to the already large number of un-assessed fisheries at a global scale. T his deficiency is more evident in the Mediterranean Sea where stock assessments are relatively fewer. A new method (AMSY) has been recently developed to assess stocks for which only abundance trends from scientific surveys are available. The AMSY method was used in the Aegean Sea to assess the status of 74 fish and invertebrate stocks (50 actinopterygians, 4 sharks, 5 rays, 12 cephalopods, and 3 crustaceans) for which catch data are lacking; 20 of them have medium or high market value and are being targeted by fishing fleets, while the remaining 54 are either not targeted, but by-caught and often discarded, or are not exploited at all. Overall, 31 of the 54 non-targeted stocks (57%) were healthy in terms of biomass (B/Bmsy > 1), whereas only 6 of the 20 targeted stocks (30%) were healthy. Of the 23 unhealthy non-targeted stocks, 12 were near healthy (B/Bmsy > 0.75), compared to only 1 of the targeted stocks, whereas 10 non-targeted stocks (19%) and 10 targeted ones (50%) were outside safe biological limits (B < 0.5Bmsy). Cephalopods and crustaceans were generally in a better status compared to fishes. The results confirm that fishing does not only affect commercial stocks, but it may also affect by-catch stocks. In general, stocks that are targeted by fishing fleets are in a worse status in terms of biomass compared to those that are only occasionally collected as by-catch or those that inhabit environments that are not accessible to fishing fleets.

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Seagrass meadows and mussel reefs provide favorable habitats for many fish species, but few studies have compared the associated fish assemblages directly and examined the influence of environmental variables. Knowledge of fish assemblages associated with disparate habitats is needed for the conservation of coastal fisheries and marine spatial planning. Catch per unit effort data derived from fyke nets showed similar species richness and diversity in seagrass meadows and mussel reefs, suggesting that both habitats support elevated marine biodiversity of mobile fauna. However, it was shown that fish assemblage structure differed between those habitats, and also fish abundance in seagrass meadows was significantly higher than in mussel reefs by comparing the data with a multivariate extension of Generalized Linear Models (GLM). Furthermore, employing underwater video recordings to compare fish abundances in high and low water current speed mussel reefs with a Generalized Linear Mixed Model with negative binomial distribution, data revealed similar fish abundances (in terms of the MaxN metric) despite the variation in current speed, probably because the mussel formations provide sufficient shelter, even from high water currents. The commercially important species Atlantic cod (G. morhua), however, was significantly more abundant in the low water current mussel reef. Therefore, restoration efforts targeting G. morhua could benefit from restoring low current mussel reefs. Our study provides input for the conservation of coastal recreational and commercial fisheries, habitat restoration and marine spatial planning where certain habitats may be prioritized.