Pond-breeding amphibians are deme-structured organisms with a population genetic structure particularly susceptible to demographic threats. We estimated the effective number of breeding adults (Nb) and the effective population size (Ne) of the European urodele amphibians Triturus cristatus (the crested newt) and T. marmoratus (the marbled newt), using temporal shifts in microsatellite allele frequencies. Eight microsatellite loci isolated from a T. cristatus library were used, five of which proved polymorphic in T. marmoratus, albeit with high frequencies of null alleles at two loci. Three ponds in western France were sampled, situated 4–10 kilometres apart and inhabited by both species. Parent–offspring cohort comparisons were used to measure Nb; samples collected at time intervals of nine or 12 years, respectively, were used to measure Ne. The adult population census size (N) was determined by mark–recapture techniques. With one exception, genetic distances (FST) between temporal samples were lower than among populations. Nb ranged between 10.6 and 101.8 individuals, Ne ranged between 9.6 and 13.4 individuals. For the pond where both parameters were available, Nb/N (overall range: 0.10–0.19) was marginally larger than Ne/N (overall range: 0.09–0.16), which is reflected in the temporal stability of N. In line with the observed differences in reproductive life-histories between the species, Nb/N ratios for newts were about one order of magnitude higher than for the anuran amphibian Bufo bufo. Despite of the colonization of the study area by T. cristatus only some decades ago, no significant genetic bottleneck could be detected. Our findings give rise to concerns about the long-term demographic viability of amphibian populations in situations typical for European landscapes.