Have you tried DAPI? Check out the attached publication:
"To improve the effectiveness of DAPI staining, we useda microwave oven heating method that was originally developed for the retrieval of antigens from paraffin-embedded tissue in immunohistochemical staining (Shi et al. 1991). The addition of this microwave oven treatmentto the DAPI staining method effectively eliminated the effect of the thick cell walls, and allowed DAPI to stain the cell nucleus." (referring to algae)
In addition to DAPI, acridine orange is also used to stain nuclei of coccoidal algae . Lipophilic dyes such as Nile Red (Nile Blue Oxazone), BODIPY ( 4,4-difluoro-4- bora-3a,4a-diaza-s-indacene ) or DiO ( 3,30 -dioctadecyloxacarbocyanine perchlorate) are also used to stain algal cells
Khem Chand Saini Yes, Hoechst has been used for labeling algae. Here's an example paper. Perhaps they have some protocol information: https://link.springer.com/article/10.1007%2Fs00284-008-9150-8