Abstract Background The synaptonemal complex (SC) is a proteinaceous tripartite structure used to hold homologous chromosomes together during the early stages of meiosis. The yeast ZIP1 and its homologues in other species have previously been characterised as the transverse filament protein of the synaptonemal complex. Proper installation of ZYP1 along chromosomes has been shown to be dependent on the axial element-associated protein, ASY1 in Arabidopsis. Results Here we report the isolation of the wheat (Triticum aestivum) ZYP1 (TaZYP1) and its expression profile (during and post-meiosis) in wild-type, the ph1b deletion mutant as well as in Taasy1 RNAi knock-down mutants. Ta ZYP1 has a putative DNA-binding S/TPXX motif in its C-terminal region and we provide evidence that Ta ZYP1 interacts non-preferentially with both single- and double-stranded DNA in vitro. 3-dimensional dual immunofluorescence localisation assays conducted with an antibody raised against Ta ZYP1 show that Ta ZYP1 interacts with chromatin during meiosis but does not co-localise to regions of chromatin where Ta ASY1 is present. The Ta ZYP1 signal lengthens into regions of chromatin where Ta ASY1 has been removed in wild-type but this appears delayed in the ph1b mutant. The localisation profile of Ta ZYP1 in four Taasy1 knock-down mutants is similar to wild-type but Ta ZYP1 signal intensity appears weaker and more diffused. Conclusions In contrast to previous studies performed on plant species where ZYP1 signal is sandwiched by ASY1 signal located on both axial elements of the SC, data from the 3-dimensional dual immunofluorescence localisation assays conducted in this study show that Ta ZYP1 signal only lengthens into regions of chromatin after Ta ASY1 signal is being unloaded. However, the observation that Ta ZYP1 loading appears delayed in both the ph1b and Taasy1 mutants suggests that Ta ASY1 may still be essential for Ta ZYP1 to play a role in SC formation during meiosis. These data further suggest that the temporal installation of ZYP1 onto pairing homologous chromosomes in wheat is different to that of other plant species and highlights the need to study this synaptonemal complex protein on a species to species basis.