Assessing genetic diversity is essential for the characterization and conservation of livestock. This study investigates the genetic diversity of the three indigenous goat breeds from northern Belgium (Flanders), Kempische Geit, Vlaamse Geit, and Belgische Hertegeit, using pedigree and genomic data. Pedigree analyses estimated inbreeding and effective population size, while genomic data were assessed using runs of homozygosity (ROH) and population structure analyses (F st , principal component analysis (PCA) and ADMIXTURE). Pedigree-based results revealed moderate inbreeding (F ped = 10.3%, 7.4%, and 9.0%) and critically low effective population sizes (N e = 17, 28, and 43, respectively). Despite these constraints, population trends since 2017 show encouraging growth, with active breeding females increasing 153% (Kempische Geit) and active breeders rising 90% (Vlaamse Geit). Genomic data from 280 individuals (88–97 per breed), genotyped using the GGP Goat SNP array, revealed inbreeding coefficients based on ROH from 8% to 15%, with individual values reaching up to 39%. Several ROH islands were detected, including two in Vlaamse Geit on chromosomes 10 and 13, which overlap with regions reported in other international breeds. Linkage disequilibrium-based estimates of effective population sizes (N e = 21–22) further highlight the endangered status of these breeds. Genetic differentiation was substantial (F st from 0.10 to 0.14) which was supported by PCA and ADMIXTURE. This study provides the first integrated pedigree and genomic assessment of goat diversity in Flanders, offering critical insights for the conservation and sustainable management of these local breeds. These data support comparisons with international populations and inform future breeding strategies. • Flanders (Northern Belgium) has three local goat breeds • All three goat breeds were analyzed based on pedigree and genotype data • Inbreeding coefficients based on runs of homozygosity were between 8% and 15% • Effective population sizes remain below critical thresholds for viability • The three goat breeds are considered endangered