Aims: Two Bacillus thuringiensis collections from terrestrial and aquatic habitats were compared in order to study the possible interrelationships between habitat and biological characteristics (serovar, cry genes content and toxicity). Methods and Results: Bacillus thuringiensis strains were characterized by serology, PCR, and one-dose treatment against the noctuids Helicoverpa armigera and Spodoptera exigua, and the dipteran Tipula oleracea. A total of 12 and 10 different serovars were identified within terrestrial and aquatic strains, respectively. The number of non-toxic strains was greater in aquatic (41.6%) than in terrestrial habitats (5.3%). The genes cry1C, cry1D and cry1E were significantly more frequent in the terrestrial habitat. The cry1B gene was very frequent within thuringiensis strains. Conclusions: A high diversity was found in terms of serovars present and cry genes content in both collections. The relative frequency of individual cry genes was different in both collections, and a serovar-dependent distribution of the cry1B gene was found. Some strains sharing the same set of cry genes differed in their toxicity, suggesting important differences in gene expression. Significance and Impact of the Study: The inter-relationships between serology, cry gene content and toxicity may allow a better understanding of B. thuringiensis ecology.