Comparative analysis by RNA oligonucleotide fingerprints of total genomic RNA as well as the individual RNA segments of equine 2 influenza A virus strains from 1963, 1968, 1979, 1984, 1987 and 1988 revealed genetic diversity. Strains from the epizootic outbreak during 1978-1979 showed minor differences among their genomes. The Swedish isolates from 1979 up to 1988 showed increasing genomic heterogeneity indicating genetic drift.