Genetic variability in the Krškopolje pig population was estimated with the objective to set directions for effective conservation program. Pedigree data was used for this study. To evaluate genetic structure, we used long established (Wright, Malecot) as well as recent approaches (MacCluer, Boichard, Ballou, Kalinowski, Baumung). Software packages SAS/STAT, PEDIG, CFC and Mendel were applied for pedigree analyses. Pedigree file included 2,940 animals born in years 1992 to 2017. Standard deviation of family size in sires was 6.72 offspring, showing very unequal number of mattings per boar. Average generation interval was 2.56 years. Because the proportion of known ancestors, average complete generation equivalent and pedigree completeness index have increased over time, the estimates of inbreeding coefficient and effective population size are more reliable. The average coancestry in the reference population was 13.95% and the average inbreeding coefficient was 4.0%. The effective population size was estimated to 51, indicating that the population is endangered. Estimated genetic diversity reduction due to the random genetic drift and unequal founder contributions was 6.7%. Estimated correlation between Wright's (i.e. standard) inbreeding coefficient and Kalinowski’s coefficient of recent inbreeding was 0.99, suggesting that the majority of inbreeding in the reference population occurred in recent years. The estimates of partial coefficient of inbreeding and partial coefficient of ancestral inbreeding have shown that eleven founder lineages contributed the majority of inbreeding. Results from gene dropping analysis are probabilities of extinction, high risk of extinction and future extinction of founder alleles; at least alleles from 25 founders are entirely lost for today's population of Krškopolje pig. Special attention should be paid to the preservation of descendants of those founders whose alleles are the most likely at risk. Results obtained in this study allow managing the genetic pool of population and contribute to conservation of the genetic diversity of the only indigenous pig breed in Slovenia.