A method for determining effective population size in organisms with arbitrarily complex life-histories, including clonal reproduction, is developed. A coalescent model that focuses on the time at which two alleles last shared a common ancestor leads to a method for determining an inbreeding effective population size. Comparisons with previously developed approximate methods for haploid age-structured models show close, but not exact, agreement. A diploid population with both clonal and sexual reproduction is considered; examples from published demographic studies are used to show the effects of within-individual versus between-individual coalescence times and different definitions of generation time in calculating effective population size. These examples show relatively small differences in effective population sizes calculated using within- and between-individual coalescence times; however, in one case, different definitions of generation time lead to a large change in ratios of effective population size to census size (Ne/N). The Ne/N calculated for clonally reproducing organisms in this paper seem to be substantially smaller than published values for organisms lacking clonal reproduction.