Overall, the analysed samples show a heavier reliance on fish found around coral reefs than other habitats; however, the proportions of exploited habitats vary among samples (Figure 3). Fish that are observed to inhabit various inshore habitats occur in high numbers (56% of total). This category is largely composed of emperor fish (Lethrinus spp., 55%), a diverse genus in this region that is also a very commonly exploited fish. It includes species from a range of inshore habitats, but without more detailed identification, the genus can only be classified in the 'various' category. It was included in the analysis because it represents a significant proportion of the exploited fish (32% of the total sample). The majority of fish taxa that can be associated with a particular habitat are found in or around coral and rocky substrates (24% of total). The proportion of these fish is greater in the samples from the offshore islands (40–84%) but much smaller in the sample from Shanga (17%). At Shanga, fish found in estuarine habitats are more common (21%) than at the other sites, although this habitat is also represented in some of the off-shore island samples: Ras Mkumbuu (12%), Unguja Ukuu (8%), and Tumbatu (2%). Fish from the outer reef and sandy-muddy floors are also present in some of the samples in smaller numbers. In particular, open sea species are only present in the samples with material from the second millennium.
The composition of fish taxa within the habitat categories reveals other differences in the exploitation of marine habitats. Common coral species vary across the samples: trevally (Caranx spp., 21%) is the most numerous coral-associated taxa at Mtambwe Mkuu; while parrotfish (Scarus spp.) dominate the coral category in the Shanga (36%), Unguja Ukuu (33%), and Fukuchani (38%) samples. Fishers use different fishing gear to exploit these fish species, particularly between parrotfish and trevallies: parrotfish are often caught in basket traps and seine nets while trevallies are caught with hand lines, stationary gill nets, and ring nets. The strategies fishers use to exploit emperor fish include hand lines, basket traps, and seine nets. Estuary fish at Shanga are mostly marbled parrotfish (Leptoscarus vaigiensis, 71%), a species found in sheltered bays, harbours, and lagoons that feeds on seagrasses and algae (Froese and Pauly 2012). The marbled parrotfish, which is a species only identified in the Shanga sample, is particularly associated with basket trap and spear fishing in the Lamu study. The large proportions of parrotfish species in the Shanga sample in both estuary and coral habitats suggest that trap fishing was a particularly important fishing strategy in that region. Offshore island samples, all of which tend to have higher proportions of coralline fish, also show different patterns in exploitations strategies. At Mtambwe Mkuu, for example, the high percentage of trevally sets it apart from the other offshore samples. These differences could represent variability in the natural distribution of fish along the coastline, the use of different fishing technologies or a combination of both.
It was possible to compare the changing exploitation of habitats over time at Shanga because the data cover a longer period divided into a series of phases. Although the high proportion of Lethrinus spp. in this sample was classified in the 'various' category, it is clear that estuary and coral habitats were important fishing areas over time and that there is a significant increase in open sea/outer reef fish in the second millennium AD (Figure 4). The majority of fish in this category are grey sharks (Carcharhinus spp.) plus one occurrence of longfin mako (Isurus paucus), identified from a tooth (Horton and Mudida 1993, 692). Longfin mako is an oceanic shark species with an average size of 200cm in total length that approaches land to give birth; grey sharks are the most common type of shark found in this region and includes shark species that are known to venture closer to shore to feed (Froese and Pauly 2012; Fischer and Bianchi 1984). It is possible that these open-sea species were caught near the shoreline; however, they are associated with a different set of fishing strategies than most inshore fish: long lines and drifting gillnets that are used in offshore waters (Table 2).