The caddisfly community composition and structure were studied in the Mediterranean (i.e., central part of Herzegovina) and the temperate (i.e., Central Bosnia) regions of the country which differ considerably regarding the climate, hydrology, geomorphology, and vegetation. In both studied areas, four rivers with seven sampling sites each were selected for light‐trapping of adult caddisflies during a one‐year period. A total of 97 species were collected (i.e., 52 in Herzegovina during 2003 and 67 in Central Bosnia during 2004) and seven of them are first records for Bosnia and Herzegovina. Marked differences in caddisfly community composition and structure between the two regions were found and confirmed by a cluster analysis of comparable river sites. These differences could be primarily linked to observed variability in environmental factors. Also, distinct phenological patterns of caddisflies were found in the Mediterranean and temperate parts, respectively, and these were further analyzed in detail for the five most abundant common species. For the populations in Central Bosnia, generally later and shorter periods of flight were recorded. Therefore, we tested the influence of meteorological parameters (night air temperature during the light‐trapping, and monthly values of air temperature, precipitation, humidity, cloudiness, and wind speed) on flight activity and periodicity of caddisflies in both regions. Air temperature proved to be the most important of tested parameters influencing caddisfly flight patterns (rs > 0.87 for monthly values and rs > 0.44 for air temperatures during light‐trapping; p < 0.001). Thus, temperature during light‐trapping and minimum monthly values seem to be important for the flight of caddisflies, since these values were significantly different (p < 0.001 and p < 0.05, respectively) in the two regions of the country. Additionally, in this paper we will discuss some implications for conservation of caddisflies due to the predicted climate change.