Illex coindetii is the most common benthic ommastrephid squid exploited by bottom trawl in the Mediterranean Sea. A recent study examining trends in population metrics based on data from the International Bottom Trawl Surveys in the Mediterranean (MEDITS) has shown an increasing trend in average lengths of I. coindetii sampled in the eastern Ionian Sea, suggesting that this is possibly due to the thermoaline circulation reversal and the warming of the entire water column in this area after 1998 because of the Eastern Mediterranean Transient (EMT). In this study, spatial and inter-annual variability of the population structure and the distribution patterns of I. coindetii in the eastern Ionian is investigated in relation to environmental characteristics. Datasets used include demographical and biological data derived from the MEDITS surveys carried out during the summers of 1994-2006 and environmental parameters obtained through CTD sampling and remotely sensed imagery. Analyses performed include descriptive methods like the length frequency analyses and GIS mapping of standardized densities, as well as habitat modelling of presence data for different life stages of I. coindetii (based on generalized additive models and maximum entropy). An increasing trend in frequency of occurrence and density indices for all life stages has been detected during the studied period, being more evident after 1999. At the same time a temporal shift in seasonal maturation was also evidenced, coinciding to the warming of eastern Ionian waters due to EMT effects. Spawning aggregations occurred steadily on the upper slope of the relatively more protected area west of the Kefalonia Island, extending also over the lower shelf of the Patraikos Gulf in summers with lower upwelling activity. The inter-annual variability observed in the location of main recruitment areas could be related to mechanisms affecting post-hatching dispersal during late winter and spring, when maximum intensity of surface mesoscale activity has been observed. Depth was found the principal variable associated with the distribution of I. coindetii in the study area. Anomalies of surface temperature and chlorophyll-a, as well as distances from coast and thermal fronts were also selected for the final set of response variables without, however, showing any clear trend particularly in the case of recruits. The results of this study highlight the importance of a more comprehensive study of both environmental processes and I.