Different almond (Prunus dulcis) cultivars have been characterized by their contrasting shoot branching patterns; however, the differences between patterns have been difficult to quantify. This study aimed to model the branching patterns of 2-year-old proleptic shoots on three almond cultivars (Nonpareil, Aldrich, and Winters) representing different tree architectures. The effects of branching pattern on flowering were also studied. The branching patterns of shoots of different length categories were assessed by a single hidden semi-Markov model for each cultivar. The models identified zones of homogeneous branching composition along shoots and were used to extract the occurrence and number of nodes of the zones according to shoot length categories. The numbers of flower buds were also determined for each shoot length category in each cultivar. The models of branching patterns of ‘Nonpareil’ and ‘Aldrich’ were similar and differed from the ‘Winters’ model. ‘Winters’ shoots produced more zones, but some of the zones had similar characteristics as previous zones and thus appeared to be repeated. This cultivar also had more spurs and sylleptic shoots than the other cultivars. The occurrence and node number of the central zones decreased along with reduction in shoot length in all the cultivars. ‘Aldrich’ tended to have more flower buds than comparable-length shoots of the other two cultivars. This study provides a quantitative description of the shoot branching patterns of three important cultivars and explains how branching changes in relation to shoot length, whereas production of flower buds varies despite similar branching patterns.