In recent years, new methods have been developed for the molecular typing of Leishmania that need to be extensively validated by studies of clinical isolates in a well defined epidemiological context. The present study is a contribution to this effort. Using PCR-RFLP of gp63 and cpb genes, we analysed 59 isolates of L. (L.) infantum obtained from different regions of Algeria and originating from different clinical forms, hosts and zymodemes. PCR-RFLP identified 15 different genotypes among the four zymodemes analysed, thereby demonstrating a higher discriminatory power than multilocus enzyme electrophoresis. We did not see any significant relationships between PCR-RFLP patterns and host origin. However, cpb polymorphism showed two interesting trends: a possible relationship with the cutaneous origin of the isolates and an association with a West-East cline. We verified the proof of evidence of the direct applicability of gp63 and cpb PCR-RFLP in blood samples from dogs. Further work is needed to compare the sensitivity of pattern detection with cpb and gp63 PCR-RFLP but our results pave the way to future multilocus PCR-RFLP studies of L. (L.) infantum populations.