Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast  Schizosaccharomyces pombe . Both killers belong to the previously uncharacterized  wtf  gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of  wtf  genes vary considerably between  S. pombe  isolates, indicating rapid divergence. We propose that  wtf  genes contribute to the extensive intraspecific reproductive isolation in  S. pombe , and represent ideal models for understanding how segregation-distorting elements act and evolve.