In this report, we describe the partial molecular characterisation of Plasmodium falciparum isolates obtained from two individuals who were involved in a probable case of accidental malaria transmission after admission to a hospital in the metropolitan area of São Paulo, Brazil. Molecular analysis of polymorphic stretches of the merozoite surface protein 1 and 2 genes using PCR-typing and nucleotide sequencing revealed that the two isolates were identical and that the identified msp-1 gene was different from all others published to date. Additional anamnestic data supported our findings and made all other possible routes of infection unlikely. The methodology used here is simple to perform and needs as little as one Giemsa-stained blood smear as starting material.