Understanding the rates, spectra, and fitness effects of spontaneousmutations is fundamental to answering key questions in evolution, molecular biology, disease genetics, and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone. By sequencing 30 genomes and implementing a series of validation steps that informed the bioinformatic analyses, we identified a total of 477 single nucleotide mutations (SNMs) in the MA lines, corresponding to a mutation rate of 2.30 x 10(-9) (95% CI 1.90-2.70 x 10(-9)) per nucleotide per generation. The high overall rate of loss of heterozygosity (LOH) of 4.82 x 10(-5) per site per generation was due to a large ameiotic recombination event spanning an entire arm of a chromosome (similar to 6Mb) and several hemizygous deletion events spanning similar to 2 kb each. In the non-MA population, we found significantly fewer mutations than expected based on the rate derived from the MA experiment, indicating purifying selection was likely acting to remove new deleterious mutations. We observed a surprisingly high level of genetic variability in the non-MA population, which we propose to be driven by balancing selection. Our findings suggest that both positive and negative selection on new mutations is powerful and effective in a strictly clonal population.