Ten isozyme genes were studied after analyzing the variability of eight enzyme systems—glucose phosphate isomerase (GPI), phosphoglucomutase (PGM), aspartate aminotransferase (AAT), leucine aminopeptidase (LAP), 6-phosphogluconate dehydrogenase (6PGD), isocitrate dehydrogenase (IDH), shikimate dehydrogenase (SDH), and aconitase (ACO)—in the progeny of five crosses among almond [Prunus amygdalus Batsch, syn. P. dulcis (Miller) D. A. Webb] cultivars. Six of these loci were found to be located in two linkage groups, one containing four loci (Pgm-2, Gpi-2, Aat-2, and Lap-1) and two more in the other (Idh-2 and Aat-1). Genetic configurations of pairs of loci specific to segregating F1 progeny of crosses between heterozygous parents were found in our data, for which we derived the estimate of the recombination fraction and its variance. Linkage data for the gene pairs that could be estimated in various crosses were used to obtain a joint estimation of the recombination fraction.