Three brook charr full sib families were genotyped for 133 microsatellite loci and two 'Clock' genes, resulting in the identification of 43 linkage groups, 35 of which contain two or more markers. While only twelve conserved homeologous linkage groups were identified between brook charr and rainbow trout and six between brook charr and Atlantic salmon, nearly all of the highly supported rainbow trout and Atlantic salmon homeologies were identified. QTL for time to hatch (TTH) were identified in genomic regions of brook charr showing homology to four of the five linkage groups in rainbow trout where QTL for TTH were identified. Additionally, several of the QTL for TTH have been identified in regions of the brook charr genome showing homology to rainbow trout and/or Arctic charr linkage groups associated with maturation timing and/or spawning time. The locations of putative candidate genes in relation to brook charr TTH QTL are discussed.