Summary Background Atopic allergy has been more common among schoolchildren in Finland, as compared to Russian Karelia. These adjacent regions show one of the most contrasting socio‐economical differences in the world. Objective We explored changes in allergy from school age to young adulthood from 2003 to 2010/2012 in these two areas. The skin and nasal microbiota were also compared. Methods Randomly selected children from Finnish (n = 98) and Russian Karelia (n = 82) were examined in 2003, when the children were 7–11 years of age, and again in 2010 (Finnish Karelia) and 2012 (Russian Karelia). We analysed self‐reported allergy symptoms and sensitization to common allergens by serum sIgE values. The skin (volar forearm) and nasal mucosa microbiota, collected in 2012 (aged 15–20 years), identified from DNA samples, were compared with multivariate methods. Results Asthma, hay fever, atopic eczema, self‐reported rhinitis, as well as atopic sensitization, were threefold to 10‐fold more common in Finland, as compared to Russian Karelia. Hay fever and peanut sensitization were almost non‐existent in Russia. These patterns remained throughout the 10‐year follow‐up. Skin microbiota, as well as bacterial and fungal communities in nasal mucosa, was contrastingly different between the populations, best characterized by the diversity and abundance of genus Acinetobacter; more abundant and diverse in Russia. Overall, diversity was significantly higher among Russian subjects (Pskin < 0.0001, Pnasal‐bacteria < 0.0001 and Pnasal‐fungi < 0.01). Allergic diseases were not associated with microbial diversity in Finnish subjects. Conclusions and Clinical Relevance Differences in allergic phenotype, developed in early life, remain between populations. A parallel difference in the composition of skin and nasal microbiota suggests a potential underlying mechanism. Our results also suggest that high abundance and diversity of Acinetobacter might contribute to the low allergy prevalence in Russia. Implications of early‐life exposure to Acinetobacter should be further investigated.