There has been a lot of discussion about the int vs nan problem in the past, here one issue #1194. My question for xarray-devs would be too, if there is some idea on adapting to the pandas scheme?

In the time being, you might just go the other way round (isel before where) and this little hack:

```python

overwrite fill_values with 0

sub = xr.where(z_indices == fill_value, 0, z_indices)

isel with sub and mask with where

indexed_array = val_arr.isel(z=sub).where(z_indices != fill_value) `` Update: Nevermind, this will make theindexed_arraya float. You might use the samewhere-machinery and overwrite with afill_value ` of your liking:

```python

overwrite fill_values with 0

sub = xr.where(z_indices == fill_value, 0, z_indices)

isel with sub and mask with where

indexed_array = val_arr.isel(z=sub) indexed_array = xr.where(z_indices == fill_value, fill_value, indexed_array) ``` I can't immediately see, but there might be a cleaner way to achieve this.